St Andrews Lynx

Maybe. But, look: if you give the student a bad grade and tell them off for their misogyny (or whatever), you open yourself up to a lot of unpleasantness that's well above your pay grade (complaints to the dean, to media outlets, a lawsuit [with near-zero chance of success, but still], etc.). Even if you just grade it as I suggested above, you can still be almost certain that the grade will be disputed. And that means an angry student coming to your office hours and being unpleasant (perhaps even aggressive, especially if he's a man and you're a woman), and then going to the instructor to demand a re-grade. At that point, if the instructor doesn't want to deal with it then they will give the paper a better grade and move on. But if that happens, then what little authority you have as a TA has just been significantly undermined. And that news will get around to the other students in the class, and make it into your reviews at the end of the year (especially if you're a woman): you'll get a bunch of comments about how you're a biased grader and don't know what you're talking about. So there isn't really any pitfall here: that could happen regardless of what you do, but if you let the instructor deal with it then you're safe from any potential negative consequences.
It's far better and safer for you, as a TA, to short-circuit that chain of events. If you get an egregiously offensive paper, send it up the pipeline. The instructor will then deal with it as they see fit, and you won't have exposed yourself to any backlash or erosion of your authority. My experience has always been that the instructor is on their TA's side in almost any dispute (for one thing, it's way easier for them to stand by their TAs). I'm sure there are exceptions but they're rare, they're not the norm. Besides, if you're teaching feminist theory or some other feminist class, the odds are really, really good that the instructor will have the exact same problems with the paper as you did.
Remember, you're a TA. You're paid to grade and to lead discussion sections (or whatever else is in your contract), not to change students' minds or ensure that justice prevails in the world. I know that doesn't sound glorious or especially attractive, but it's true. You're a university employee, and you have to cover your own ass. It's not worth the potential fallout to handle it yourself unless the instructor tells you to do so. 

The best way to put out a fire is to starve it of oxygen. If there's a student trolling for attention (which it certainly sounds like this one is)...minimise the attention you give them. It sounds like the only reason this student has joined the Feminist class is to be edgy and controversial - not because they need the course/grades or want to learn about the subject. 
Deal with them the way you'd deal with a student who is dominating the discussions. "Thank you for your contribution, is there anybody else who would like a chance to speak?" As a TA don't get side-tracked into arguing with this student, and don't let the other students get side-tracked into arguing with them to the point where the class is derailed. Don't act like you're shocked or upset by what they say - thank them politely for offering their opinions and move on. It's possible this student doesn't believe what they are saying anyway...but if they are, you aren't going to "save" them through force of argument. 
Follow what others have said about grading their papers or dealing with hate speech. But understand what they're really after...and don't give it to them.

The best way to put out a fire is to starve it of oxygen. If there's a student trolling for attention (which it certainly sounds like this one is)...minimise the attention you give them. It sounds like the only reason this student has joined the Feminist class is to be edgy and controversial - not because they need the course/grades or want to learn about the subject. 
Deal with them the way you'd deal with a student who is dominating the discussions. "Thank you for your contribution, is there anybody else who would like a chance to speak?" As a TA don't get side-tracked into arguing with this student, and don't let the other students get side-tracked into arguing with them to the point where the class is derailed. Don't act like you're shocked or upset by what they say - thank them politely for offering their opinions and move on. It's possible this student doesn't believe what they are saying anyway...but if they are, you aren't going to "save" them through force of argument. 
Follow what others have said about grading their papers or dealing with hate speech. But understand what they're really after...and don't give it to them.

The best way to put out a fire is to starve it of oxygen. If there's a student trolling for attention (which it certainly sounds like this one is)...minimise the attention you give them. It sounds like the only reason this student has joined the Feminist class is to be edgy and controversial - not because they need the course/grades or want to learn about the subject. 
Deal with them the way you'd deal with a student who is dominating the discussions. "Thank you for your contribution, is there anybody else who would like a chance to speak?" As a TA don't get side-tracked into arguing with this student, and don't let the other students get side-tracked into arguing with them to the point where the class is derailed. Don't act like you're shocked or upset by what they say - thank them politely for offering their opinions and move on. It's possible this student doesn't believe what they are saying anyway...but if they are, you aren't going to "save" them through force of argument. 
Follow what others have said about grading their papers or dealing with hate speech. But understand what they're really after...and don't give it to them.

The best way to put out a fire is to starve it of oxygen. If there's a student trolling for attention (which it certainly sounds like this one is)...minimise the attention you give them. It sounds like the only reason this student has joined the Feminist class is to be edgy and controversial - not because they need the course/grades or want to learn about the subject. 
Deal with them the way you'd deal with a student who is dominating the discussions. "Thank you for your contribution, is there anybody else who would like a chance to speak?" As a TA don't get side-tracked into arguing with this student, and don't let the other students get side-tracked into arguing with them to the point where the class is derailed. Don't act like you're shocked or upset by what they say - thank them politely for offering their opinions and move on. It's possible this student doesn't believe what they are saying anyway...but if they are, you aren't going to "save" them through force of argument. 
Follow what others have said about grading their papers or dealing with hate speech. But understand what they're really after...and don't give it to them.

Teachers can report hate speech in papers. I would deal with this by grading strictly based on the req's I've laid out in the paper, reporting if necessary, and keeping a thorough record of each correspondence with the student in question. Normally, hate speech isn't backed up through credible sources, making it very easy to grade down. Back up your notes and keep everything (honestly, even the students that don't cause issues in class might still raise a ruckus about grades later). As for trying to preemptively stop this problem, include something in the green sheet explicitly stating that hate speech will not be tolerated and students need to be respectful in their discussions inside your class. You don't need to agree with each other, but you should support your disagreements with fact and never devolve into attacking the other person. That gives the professor recourse to discipline the student if necessary (discipline here could mean reminding them of the rules and making them back off to kicking them out of the class for that period if necessary). Differences of opinion can be great for a class if the discussion of those differences is respectful, but it's part of a teacher's job (imo) to keep order in the class (and keep it relatively safe for those present).

This is definitely okay! Usually the "dedication" is something short and either whimsical or serious/formal (i.e. just one or two lines like fuzzy's example) and the "acknowledgments" are longer. Most schools do not place any requirements on the acknowledgements you want, and it's one of the few places where you have almost absolute freedom to write whatever you want. Even the most formal scholar would likely write something personal here, I think.
In my acknowledgements, I dedicated one paragraph for my advisors, current and past, one for my friends and two for family. I always find the acknowledgments the most fun part of the thesis to read. And, as you might have seen quoted (but never backed up with stats), the acknowledgement is often the first and only thing that people read. Anecdotally, I know that I have purposefully looked up dissertations only to read their acknowledgments. Personally, I feel that in the sciences, we do too much "depersonalization" of science and I think there is no need to overly distance ourselves from our work. So, I purposely seek out dissertation acknowledgments to get a peek at someone's personal / more human side.
If you check your dissertation requirements, you might find even more opportunities to personalize your dissertation, if that's what you want to do. For example, although the thesis template provided by the school didn't have a placeholder for a front matter quotation, I found that in the policies, this is an optional section that's allowed. So I added a quote that has inspired me most of my adult life and really kept me going through grad school (I just have a page with the quote there, with no explanation of it). One of my committee members had a picture of his cat on his dedication page (the thesis was also dedicated to his cat). 
Finally, while not recommended for everyone, many people I know have snuck little inside jokes or references into the actual text of their dissertation. Sometimes they are subtle but sometimes they are not! I've read one where after a long paragraph on math, the text reads something like, "If you're one of my committee members and you are still reading along, let me know and I'll buy you a drink." (the person later told me that only one of their committee members said they saw that line). I think this is pretty funny and it's great that people feel like doing this. Personally, I enjoy seeing this type of humour but I don't enjoy producing it myself, so I kept the main body strictly scientific. But that's just me. Given your other posts here with your worries about the text, you probably don't want to do something like that yourself, but just letting you know what I've seen out there.

Sounds like you'd never need to even ask this person for a letter. I wouldn't. So you just need to know that he won't actively seek to harm you by reaching out to people and bad-mouthing you behind your back. That would be an unlikely and extraordinary step for someone to take, so I don't think it's something to lose sleep over. But to be on the safe side I think it's probably best to stay the hell away from this person, so they can find someone else to get pissed at. It doesn't sound like there's any kind of long-standing grudge against you, so hopefully out of sight, out of mind. 
At the same time, you might take this as a lesson about how situations like this one can get out of hand. What the prof did is *not* okay, but it's a potential teachable moment: when you create a written record (email) and distribute it widely, people can use it not as you intended. Conversations are often better as a first step to solving disputes like this, especially when it's not clear to me that it's your place as a grad student to instruct undergrads on what they should or shouldn't do (unless you have some official capacity that allows you to do that). It's also unfortunately often the case that the power structure of workplaces (academia included) is such that you need to pick your battles wisely and sometimes doing a little extra work is better than engaging in a fight with a superior. When you choose to criticize how someone does their job, you can expect pushback, even if you're entirely correct, so you should always factor that into your plans. This is not criticism of what you did, just a suggestion for learning from it. You can choose to pursue this problematic culture in your department, but you should do it fully aware of your position in the pecking order and how much you opinion counts. If you aren't in an obvious position to bring about change, it's worth thinking about how you can still influence things in a positive way.

You should read up on implicit bias. It sounds like a version of that may very well be going on. It's alarming because there is research to show that letters of recommendations for female candidates are weaker than for corresponding male candidates, even if the writer isn't aware (e.g. here, but you can google for lots more). They may also get fewer opportunities, like to do with research, as you describe. (There are lots of other consequences, small and large, but perhaps less relevant here.) It's hard to know what to do about it; the best answer I know is talk about it openly as a community and take training to combat it. It doesn't fix the problem, but it reduces it and makes it manageable. It's harder when someone denies what is plain to see, but they may still benefit from a collective conversation on the hazards of not paying attention. If done, it should be at least department-wide and not targeting any particular professor (it affects everyone, regardless of gender, unfortunately). You didn't mention your field, but some fields have become very active at raising awareness of this issue. You could seek help from your field's professional society or from a local university-run organization, if one exists. No quick solutions here, I'm afraid. 

My first reaction was: Yikes. I am sad to hear about cases like this.
My second reaction was: Is this website/article the only report of this case or has it been reported elsewhere and details corroborated by another source? After the initial reaction, I went to see if I could find instances of this reported elsewhere, but did not find anything. I would be concerned that the author of this article has some personal vendetta against this person and is digging up pretty obscure details of their past. (I'm not sure if you, @Ibn Al-Haytham, is also the author of this article, or if you're just linking to it).
Summary: I don't think this is a big deal at all and I think the author of this article is presenting minor mistakes as motivated wrongdoing without any substantial evidence. Please see below for a fact check of the article. Since this post is now super long, I'm presenting my main summarized thoughts up here.
In the linked article, the author brings up a concern of CV fabrication and coverup by universities. However, the case in question is hardly clear evidence of this happening. Based on my fact-check below, there is only one instance where there could have been a deliberate attempt to claim credit for something the professor did not do, although there are plenty of benign explanations that also fit. This seems much more like a case of sloppy CV record keeping and making mistakes one really shouldn't make. And although I agree with the linked article's author that integrity is extremely important and once someone does something academically unethical, their other actions do become suspect. However, one clearly cannot group all questionable acts together. Even if the prof in question did knowingly leave the one incorrect item in their CV in an attempt to boost it, this is a very minor offense that does not lead me to question everything else the professor did. In addition, I do not think such small differences gave the prof in question any real unfair advantage. Overall, I think the linked article contains a lot of speculation, especially about the prof in question's motives, which the author cannot know. It also presents minor issues as major ones with little argument to back that up and arbitrarily decides on the worst possible outcome when facts are unknown (without acknowledging other explanations). Altogether, it seems like an irresponsible article to have published.
---- Here's what I did to fact-check the article ----
It was a long article but the two main problems the author pointed out with the CV is 1) the person in question put some conference abstracts under conference proceedings in the CV and 2) the person in question claimed authorship of 2 articles they did not author.
For #1. I don't think there is any wrongdoing here at all. Looking at the archived CV, under "peer-reviewed conference proceedings", the professor makes it clear that there are two types of things being listed, "Talk presented at ..." and "In Proceedings....". To me, this clearly shows that the ones with only "Talk presented at..." are not published proceedings. It's legitimate to call them peer-reviewed because conferences use peer review to select which abstracts are going to be scheduled as talks. In the article, the author uses their own definition of Proceedings and cites Wikipedia, but these are certainly not the only (nor the only acceptable) definition. 
For #2. I decided to do my own digging since I could not find details corroborated by any other source. The article's author objects to two publications: 
A.      Davidenko, N., Beaumont, J., Davidenko, J.M., and Jalife, J. (1997). Spatio-temporal evolution of spiral wave activity. Biophys. J. 72:2 A370, June 1997.
B.      Beaumont, J., Davidenko, N., Davidenko, J.M., and Jalife, J. (1995). A model study of changes in excitability of ventricular muscle cells with repetitive stimulation. Inhibition, facilitation, and hysteresis. Am. J. Physiol. 268; 37:H1-H14, 1995.
I started with Publication A. Unlike the article's author, I was able to easily find this publication within 5 minutes of searching. Here's what I did. I went to the journal's website. I searched back issues to look for Volume 72, Issue 2. It turns out that there was a meeting and the abstracts of presentations were published in the Biophys J. As a special issue, probably (normal in my field too). With the page number being "A370", it was just a matter of searching through the long list of PDFs organized by session to determine which one A370 belonged to. I found it on Page 22 of this file: http://www.cell.com/biophysj/pdf/S0006-3495(97)78745-9.pdf
The main problem with this line in the CV was that the published issue of Biophys J. is February 1997 but the CV says June 1997. Benign typo, or perhaps misunderstanding of dates. I have a conference presentation from 2013 that was accepted for publication as proceedings but did not appear in print until 2014 (appeared online in 2013).
The secondary problem is that despite publication in a peer-reviewed journal, at least in my field, this is not a typical peer reviewed journal article. However, this is minor issue at the level of "CV padding", not a grave ethical breach that would cause me to doubt everything about this person. It is far less serious than the original claim that the person in question simply fabricated the manuscript.
In any case, nothing to ring alarm bells about at all.
Publication B is a little more tricky. I was not able to find the publication as cited by the person in question. It may not exist or I might just not be familiar enough with this field's journals (I notice that the American Journal of Physiology has many subdivisions). The author of the article claims that Publication B as cited is a misrepresentation of another article with a similar title but a different author list. I noticed that Publication B, as cited, quotes page numbers H1-H14. Volume 268 doesn't have page H1-H14 and it doesn't even have Issue 32, as far as I know. This makes me suspect a typo. Also, while it's possible to be the first 14 pages, sometimes drafts/proofs are numbered from page 1 (or A1 or H1 or whatever). Perhaps the person in question, in 1995, when they are at an early stage of their career (an undergrad) simply did not know that the page numbers on a draft manuscript did not actually represent the final published page numbers and they just continued to copy and paste the same CV line for decades. I also know from experience that sometimes as manuscripts and projects evolve, author lists change. Maybe the person in question was removed from the author list but didn't know it. Or maybe there is another article out there and this was just a typo. Note that these page numbers and the author list appear very similar to a 1998 publication also on the CV (see: https://www.ncbi.nlm.nih.gov/pubmed/9649363). Maybe the 1995 project that the person in question contributed to was split into two works, one published in 1995 and the other part (where the author got moved to) was published in 1998. Sometimes this happens in my field because the project hit some snags or the lead author had to prioritize other things. So maybe at one point, the person in question was a co-author on the 1995 work but then failed to remove the listing from the CV after the project evolved.
Again, this is careless behaviour and disappointing to see in another academic. But at this time, the person in question was a undergraduate student and I know I made lots of dumb mistakes like that. This person should have corrected their CV once they knew better but I don't know all the details, so I can't really judge. That said, I can't rule out malicious intent like the article linked here suggested, but that's certainly not the only plausible explanation. I don't think it is a good idea for the article's author to only present the worst possible scenario and then conjure up some motivations that are not backed up in any way. It's fine to point out that the prof in question should have known better but it's a little far fetched to make the other claims. And I think it's downright irresponsible to present the worst possible case as the only scenario without even considering other explanations.

Ahhh, Facebook privacy settings can control whether posts are visible to 'Close Friends', 'Public' or 'All Friends except....' 

Okay, so there are relevant facts, irrelevant facts, and speculation. You'll do well to distinguish those in any official conversation: 
Relevant facts: 
You were on track as per your last meeting.  You were asked by your advisors to divert your attention to writing a manuscript, which you did.  This led to a slow down in dissertation writing.  At some point there was a money problem that led to a delay in the manuscript writing. Everyone agreed that you should re-focus on the dissertation.  You have been doing that, with good progress again, and a planned submission date by the end of the year.  Irrelevant facts: 
Anything to do with happened to that other student in the committee meeting.  That A called B names or vice versa.  All the business with authorship on the paper.  Speculation: 
Anything to do with delaying your graduation time for any nefarious reason (e.g., to wait for another funding cycle).  Anything to do with how you interpret someone's comments or lack thereof.  Actually, at least part of your story about authorship is probably also speculation.  Ulterior motives behind the timing of submission, where to submit, etc., beyond what you witnesses firsthand.  Stick to the relevant facts, and that should be enough. This sounds like a pretty common occurrence. Don't offer speculation if anyone "thoroughly investigates". It's fair and smart to say "I don't know, I simply did what my advisors asked and trusted in their expertise." If asked, you can say you expressed concerns that the manuscript writing was slowing you down, and that after some meetings and deliberation, and partly because of the money trouble, you all eventually agreed that you should focus on the dissertation first. Again, facts, not speculation, and no accusations. People can draw their own conclusions. 

From whom and where do you hear about these activities? Are your informants reliable sources looking out for your best interests?  Or are they playing a political game in which you're a now their pawn?  Is any profession or other organized activity in the U.S.apolitical?
These questions do not mean that your concerns aren't valid and that you're ethical concerns aren't important--the question is designed to help differentiate between the Way Things Are and the Way Things Should Be. Privileging the latter over the former can lead to heartbreak, disillusionment, and an extended stay in the private sector. (Or so I've heard. )
Here's a recommendation. (Or five. No, wait. Nine.)
Develop relationships with professors in your department and identify those who are willing to teach, mentor, or train you to handle the political aspects of your profession. In your conversations with these professors, you will need to listen to what is not said. (One of the best pieces of guidance I received came from a departmental chair. He told me that the secret to being a good departmental chair was making sure that the bathrooms had paper towels.) Find ways to tease out your conceptualization of politics in the Ivory Tower. If you you're inside a sphere that houses collection of spheres, changing in size and density over time as they bounce around, how do you get to where you want to go without getting overwhelmed? Study the policies of your department, program, parent institution, and the profession you want to join. Keep in mind that the rules of the road alone don't stop speeding, DUI, and driving on the sidewalk.  Figure out how you want to "play the game." If you want to be a professional academic, you will likely have to play the game. The sooner you figure out how you want to navigate the politics, the sooner you can start developing the skills and tools you will need. Understand your limits. Think about what you'll do as you approach them. Before you're given a choice between ethical and unethical options, you will likely encounter signposts and warning signs. If you can figure out how to identify those markers in advance, you may position yourself to protect better your interests.  Avoid the gossip, grousing, and venting of graduate students that are in your cohort and a year or two ahead (i.e. those who haven't take their qualifying exams). Those who don't know are often the ones who talk the most.  Find the rock of your department. The "rock" will be the professor or staff member to whom many turn for a empathetic ear, keen insight, wise counsel, a hand up, and, sometimes, a kick in the pants. Avoid the CHE fora. Ultimately, it's a huge pond for hippos. The most nourishing and refreashing draught of water you drink there is still going to have poop in it. Read read read posts related to the professional development of graduate students by this board's moderators, by the established professionals who occasionally post, by @telkanuru, by @TMP, and by @juilletmercredi and some of the old hands who ceased coming here years ago.

Going to be honest, it sounds like you're being really unfair to your advisor based off of your unrealistic view of them as a "superhero". 
You seem to be giving no allowances for humanity, and lashing out at them for perceived flaws that are perfectly normal. 

Based upon your comments, I think that you are at least an equal partner in the deterioration of your relationship with this professor. I think that the pressure of your impending qualifying exams may be exacerbating things. 
I recommend that you focus on your qualifying exams. Until you're finished with the exams, treat everything you can as a matter of secondary or tertiary importance. After passing your exams, do what you can to find time to rest and to heal.
After the holidays, think about grabbing a cup of coffee with this professor. If you're so inclined, look at him as he's taking a nice sip of coffee and say something along the lines of "FUCKING QUALS." If you time it right, he'll need a napkin. If you time it perfectly, coffee will come out of his nose.
Once the dust and spraying beverage settle, have a mend-the-fences conversation. 
An observation. Over the last week or so, there have been some posts in which members of this BB have expressed varying levels of distress, disappointment, hurt, or anger over a relationship with an academic. Some of the remarks suggest feelings of betrayal at a fundamental level as "good" or "strong" relationships, even friendships, seem to crash and burn in short order for unknown reasons. In many situations, the only indications of things going south are odd looks, curt comments, unanswered email messages, uncommunicative replies, or deepening silences.
A recommendation. If the previous paragraph resonates, give serious consideration to the possibility that you have badly misunderstood the nature of your relationship with the person in question. There's a certain intimacy between a student seeking advanced knowledge and trusted, established practitioners that can be misinterpreted as friendship. But here's the thing. In all but the rarest circumstances, you and the professor whom you like the most, trust the most, and has taught you the most is not your friend. At least not yet. By placing the expectations of friendship upon a professor without a clear invitation, you are crossing established personal and professional boundaries. And you are placing yourself in varying degrees of peril. (Not for nothing do I address professors by their first name with great reluctance.)
Ultimately , each person, through trial and error and even unrecoverable error (BTDT) has to figure out how to navigate successfully relationships with professors and other persons of power and authority in the Ivory Tower. Some of the established members of this BB describe the relationship in terms of a boss and a worker. Others speak of the relationship between an established professional and a colleague in training. Yet even the most elegant and articulate formulations by the wisest members of this BB capture but a part of the whole. However, one feature that the different approaches share in common is the hard won understanding and acceptance that the bonds between students and professors, as strong as they may be, do not constitute "friendship." At least not yet.
 
 
 

Update: Resolution
Well, things have gone about as well as they could. I took out my frustration cooking a complicated dinner (cooking is often my therapy), calmed my nerves, had a good sip of wine, and maybe cried a little. The next day I dove in to the problem. I contacted my advisor, the director of my department, folk I know in the overarching Graduate School. I explained to them my situation, the level of contrition that things had come to this, and solicited advice for how to proceed. Email and face-to-face meetings proceeded, though nothing as formal as a hearing; today all is resolved and I now have a NC for the course, meaning that it shows up on my transcript, but doesn't count towards my credits or GPA. Whew.
What happened - folk I know, advisor included, went to bat for me. They pressured Dr. Doom to reconsider ending my career over our spat, and he apparently assented to changing the grade to no-credit. 
What I learned:
Social capital is more important than I thought. I work hard and am a friendly person doing my best to maintain good relationships; as such, I have a very good rapport with my professors and colleagues. I massively screwed it up with Dr. Doom, and that bridge is nothing but ashes floating downstream - he won't even respond if I say "hi" in the hallway. But because of my investment of social capital everywhere else, I was able to cash it in to my salvation. Had I been the anonymous graduate student, I'm not sure if folk would have risked their own political capital to rescue me. Clearly, I spent of lot of what I banked earlier. Say NO. This whole situation arose from me trying to please Dr. Doom and agreeing to help with his personal project and allowing it be tied to our course, even though it was against my better judgement. The time commitment soon spiraled out of control and I realized there was no way I could finish any of this in a reasonable timeframe. All could have been avoided. The principle is true - grad life is busy enough, if X doesn't help you to graduate sooner or get a job, don't do it. Know your resources. Where are the rules? Who are the gatekeepers? Are processes mechanistic or fluid? I now know these things - had I known them before, I might have freaked out less. Backup. I'm sure this seems like a no-brainer to everyone and their cat - but seriously, don't be like me. Get an automatic online backup system like Backblaze, or whatever, and keep your stuff backed up. I basically lost a whole semester's worth of work because the last time I plugged in my backup drive was at the beginning of the semester. Things got busy and I just forgot to do it. Online file backup costs money, but it's a lot cheaper than the cash I'll have to spend to replace my NC course in the Spring.  Peace, y'all.

At this point I'd try getting your Graduate Program Director or Program Admin involved. See if a "no credit" can be negotiated. 
Before that do your best to get the anger out of your system: be prepared to acknowledge responsibility and propose a concrete plan for getting back on track/meeting basic program requirements. 
It's usually a hassle for professors/graduate programs to fail out their students for messing up coursework. Lots of additional paperwork involved, etc. The upside is that it is possible to negotiate your way back from the brink, and for the admin team to want that outcome as much as you do.

OP, I was in the almost-exactly-the-same situation, except, I was a postdoc and then there was the 1st year student.
At some point, during your Ph.D. (especially if you are in STEM with wet lab stuff), you are going to learned and realized that your priority is to complete a certain task (i.e. an experiment) before the day ends. That priority will be placed above you taking the initiative and teaching a new member/rotation student in the lab to do something that you do routinely. Having said that, I used to wait until a new member of the lab to show up, and then show them what experiment(s) I'm doing now/next -- not anymore. Because I realized 2 things:
1) it is to my own interest to complete my task ASAP, and there is absolutely no reason to hinder my own experiment/schedule for someone who isn't part of the project (unless I was instructed by my PI that this someone has to learn this experiment ASAP), and
2) I am not the parent of this new member -- I have no obligation to tell this student that "hey, I'm gonna do this now" for every experiment that I do, all day, 7 days a week.
That being said, my expectation (and my PI agrees) is the new student need to be proactive -- taking the initiative to shadow / learn from anyone in the lab (not just me). Others maybe busy, but scientists typically are happy to talk about their research/work, or demonstrate what they are doing to someone who is genuine interested, and seemingly passionate about their work.
The student that was in the lab was quiet and all. In the first week, I showed this student what (most of the) experiments I do, and the student get their hands on. After the first week or so, I started conducting the experiments at my own pace and schedule. I was expecting that the student would either follow up with the things that we did, or ask and/or shadow what I (or anyone in the lab) were doing. Instead of showing interest to learn what everyone was doing, this student sat and their desk quietly the whole time, for the whole week. They came in, sit at the desk, and left however many hours later. From the my perspective, this student isn't interested in what we are doing, to say the least. Granted that this student claimed they were interested in our work, but had absolutely no experience on any experiments that we do regularly.
In contrast, high school students and undergrads who I worked with were all passionate about everything that we did, and they typically stick around the lab long enough to have their own projects and go from there.

I think it's important to be realistic about your ability to make a difference and also the risks that comes to you for taking these actions. You are not helping anyone if you are acting ineffectively and harm yourself in the process.
I think it's admirable that you are passionate about these issues. I am too. But I think your naive approach here is likely to do more harm than good. More harm not only to yourself but possibly to the people you're trying to help as well. If you do get your idea up and running and people submit stories, how are you going to protect their anonymity? People often only come forward if they believe the offender (whether it's harassment or other misconduct) will be properly punished. If you promise or seem to promise this to people and you don't succeed, nothing good will happen. And the people that shared their stories are now at risk because of you.
No, the experienced people here aren't just telling you that your idea is bad because they want to protect the system or find excuses not to act. We are saying it's a bad idea because many of us have gone through similar processes or seen processes like this happen before. I completely agree with you that we should act when there is wrongdoing. I would even say that it is our moral imperative to do something if we have the power to do so. I just strongly disagree with your proposed method, mainly because I think it does more harm than good.
But I won't stop there. Let me tell you about what I know actually works! I spent 4 out of 5 years of my PhD program in my grad student government advocating for policy changes at various levels at my school. I am a big proponent of action and out of my colleagues on the government, I often land on the side of more action. We have had some successes in implementing important changes for our students. 
In addition, in my field, there were two major sexual harassment cases of faculty members that became public knowledge during my grad school career. In the end, both of these offenders are no longer employed at their schools. Student action definitely was part of the chain of events that led to these bad professors leaving their jobs, but it's not in the way you're proposing. So, instead, let me tell you a little bit more about what actually happened/worked.
First, it is important to remember that the people with actual power over the employment status of a professor are the administrators at their school. The specific administrators depend on how each school is governed. These administrators are charged with the duty of protecting their school and their community: that is, the faculty, postdocs, staff, students, etc. That is their priority and even if they have personal opinions otherwise, it would be in neglect of their duties to act against the interests of the groups they represent. 
So, an appeal for the administrators to "do something" has to take these considerations into account. What reason would these administrators have to entertain an appeal from random students across the country? It doesn't really matter what an external organization of students want---it would make no sense for a specific school's administration to cater to the requests/demands of a random group of students. Instead, the appeal must come from the groups the administrators represent or have consequences for these groups. So one external body that might sway the administrators would be the funders. Either the private organizations or the government (e.g. Title IX enforcement). These groups have impact on the campus community. This was what I was trying to leverage in my post above.
But another important group are the people at the schools themselves. The faculty at the school can influence the administrators. The students at the specific school can influence the administrators. And the students at the school can influence the faculty at the school to influence the administrators. But not an unconnected external group of students that have no power over the administrators.
In one of the cases I alluded to, the Title IX case found the professor responsible for sexual misconduct over several decades. The Title IX case complainants (the term for the people who bring the case to the Title IX office) were three people he harassed in the past and are now ranging from junior to senior scientists. After the investigation concluded and the result determined, the case became public knowledge and the media wrote about it. So there's no pretending it didn't happen. While the Title IX office determines the result of the investigation, it's another administrative body that decides the punishment. These bodies generally protect tenured professors so the original decision was a fairly light punishment. A lot of people in my field protested this injustice. Many from outside the department, but the things that caused a change were actions from people the administrators actually cared about. The grad students in the department all cosigned a letter stating that they do not feel comfortable with this faculty member in their department, advising students, teaching students. But perhaps the most powerful action, it was the faculty members in the offender's department that wrote a letter to the administrators that they lost confidence in their colleague to carry out his duties as a tenured professor and do not believe him fit for the department. This letter was signed by almost every faculty member in the department. Ultimately, because of these actions, the offender was asked to take early retirement, which he did. Note that despite these extraordinary actions against the professor, he was still not "fired". He "retired".
In another case, a very similar chain of events happened. The Title IX investigation found the offending professor guilty of sexual harassment. The administrators' punishment was a one year suspension and a committee would determine if the prof was ready to return after one year. During this one year off, the professor continued harassment via social media, so the suspension was extended another year. All of this published in the media. Even in the journal Science. Near the end of the two years, a committee of faculty members across campus was struck to determine if the professor was ready to return to campus. Through pressure from students on campus, the committee held many town halls and meetings with students to hear impact of this professor's actions on students. Many faculty members initially thinking the harassment was "minor" because it was not physical realised the mental and emotional damage done through testimony of students. I am not sure what their final decision was, but they noted to the professor that his return would cause a huge divide on campus. I don't know what else they said to him, but the offender decided to resign his tenured faculty position. Again, despite huge public and media coverage, strong testimony on campus against his return, the professor still resigned, he was not fired. And this result was an unprecedented outcome for a tenured professor.
In both cases, due process found the offender to be guilty. The administrators responsible for discipline chose something fairly light for the "convicted" tenured professor. There was public outrage and backlash from others in the field. People important to the administrators made arguments against the offender. And yet, the best we can get is that they were somehow convinced to resign or retire. And, still people in the field believe that this type of thing is not a problem. And there are still people who support the guilty party and think they were treated unfairly.
I don't mean to tell these stories to discourage you from taking any action. Or to make excuses for inaction. Instead, I want to make it more clear the obstacles in the way so that you can take proper actions that will actually help people. There is huge amounts of obstacles in the way and if you present yourself as a group able to help people, you really need to be able to deliver on your promise. If you are not doing your due diligence to ensure that you treat their information responsibly and actually lead to helpful results, you are going to cause more damage to the people that trusted you with their information. I also share these stories to convince you of a different path to action. I think the key step to convincing administrators is when their key stakeholders appeal to them for action. And their most important group are the faculty members. So instead of some likely ineffective watchdog type advocacy, I think it is far better to engage in efforts to encourage faculty members to support their students when one of them comes forward with information about a professor acting unethically and inappropriately. This could be education campaigns or other awareness. And when you do hear about a case in your field, you could provide moral and resources support for students in the affected department so that they can determine the best action they need to take for themselves.

Frankly it just sounds like he's busy and under a lot of pressure, and isn't handling it terribly well. It's probably got nothing to do with you. I understand that you don't like his tone when he's in this mood, and I can imagine that I would be the same. So that much I think is justified. That said, people aren't always good at taking criticism in real time, and especially when they're under pressure. Sounds like your conversation just pushed his buttons at a time when he wasn't ready to listen. Just like in other types of relationships, there are people who want to work things out immediately as they happen, and there are people who need to calm down and think things over before they have a conversation about what happened. If he's the latter type of person, you insisting to hash things out when he is telling you to let  them go might cause this kind of blowback. I don't know you or him, but I think that it'd probably be best if you ease off and try to have this conversation again at a later time, hopefully when whatever is on his mind is over. 
Meh, I don't know what led up to this and what he meant exactly, but again, things that are said in the heat of the moment might be things we later regrets. You might also not be in the mood to interpret him generously, given your interaction. In any event, the fact that he would be okay with you working with someone else does *not* mean he doesn't respect you. I think that good professors should always be happy to have their students meet with other profs, and if a student ends up choosing to make someone else their primary advisor, a good professor can understand and accept that and not be offended. Unless he told you he is no longer interested in working with you, I'd avoid over-interpreting anything. 
Wait, there's a long time between qualifying exams and graduating. And usually an even longer time between graduating and no longer being dependent on one's advisor (as in, unless you get a job immediately out of grad school, you'll need LORs from him for a while longer). I don't think suffering from a non-functional relationship over years is advisable. For quals, I think you don't want to touch anything at this point. I guess there are practical questions about the track record of this person and the department, but unless you have some specific concerns, I'd just leave it and concentrate on prepping for the exam. After that, when it's time to concentrate on your dissertation, there are ways of gently rotating people off the committee or replacing the chair. But I think this may be entirely premature. This sounds like out of character behavior, so why don't you give your advisor the benefit of the doubt and trust that there may be outside Life factors (or Work factors) affecting him that have nothing to do with you. It's a shame that he's not better at handling it, but this can happen to anyone, and maybe at this point you should just wait a bit to see what happens. 

Three years is a long time. Focus on continually improving as a researcher & scholar, and don't worry too much about grades in coursework (those aren't the most important things in grad school). If your advisor says nothing, then my guess is it isn't a big issue for him. 

Thank you both for your thoughtful advice. I really appreciated your fresh perspective. No one else is spoken to presented suggestions quite so well. If anyone is curious about how it turned out, I am pleased to share. 
I did ask my advisor about the situation, and she too voiced a concern that the coordinating professor for the teaching position might be offended if I asked to quit in the Spring for a research position. My advisor especially noted that as a coauthor I needed to be extra careful in handling this. However, she instructed me to speak with the coordinating professor immediately and be upfront in assuring said professor that if it inconvenienced or upset her that I would absolutely turn down the research position with no questions asked. 
I was extremely nervous walking into that conversation, but turned out my worries were not warranted. The coordinating professor did find the request odd and told me that typically this is a year commitment and she would hold me to it. However, the circumstances just so happen to be that the 5 positions teaching positions that we currently have for the fall are not all needed for the Spring. In fact, the department only need 4. Despite only needing 4, the department was trying to make 5 positions for the Spring just to ensure no one loses funding. Therefore, the coordinating professor was happy to release from the teaching position into the research position. It actually worked better for everyone involved.
I am aware that I lucked out in this case  this situation could have gone badly. However, I also wish I'd been more secure and less worried about having the conversation with her. The coordinating professor and I are very close, and I honestly don't think she would have held it over my head for simply asking had it not been possible.
 

@serenade
Congratulations on earning an opportunity to pass your qualifying exams! You have shown a tremendous amount of courage by having these conversations with your professors.
As for your questions.
Only retake those parts of the exam that you absolutely have to and not one question more. Getting ready for your oral exam is plenty to do. I don't know that anyone should study 100% of the time for anything under any circumstances -- that level is not sustainable. I recommend breaking up your studying into realistic chunks of time and maybe doing some job hunting. Think carefully about pushing the exam to January. Do you want to go through the holiday season in this state of liminality?  Don't worry about what your committee members are not doing, focus on what they ARE doing. They are going to let you take all or part of the exam over. Yes, meeting with them before you retake the exam would be preferable, but as that's not an option, it's time to come up with a plan B. May I recommend: Review all of their written and verbal feedback on your qualifying exams as well for other papers and tests they've evaluated. Write down the questions you were asked during your initial oral exam with notes on how you answered and how, in retrospect, you would have liked to have answered. Track down ABDs who have had any of your committee members on their committees and pick their brains. Develop a list of potential questions that they may ask you on the oral exams.  Figure out if there are other professors who can/may/want to talk to you about preparing for your oral exam. Start a thread in the history forum of this BB. In the OP, provide a link to this thread. Perhaps stalwarts including @kotov @maelia8 @telkanuru and @TMP will provide support on line or off line.  Find three (or more) people with whom you can sand box the oral exam -- as in do a couple of test runs. A comment. Your committee members' decision not to talk to you about the exam may be part of the ritual of qualifying exams. IME, professors gave varying levels of grief to graduate students who were taking quals. What ever their motivation, I recommend taking it in stride and driving on.

In your conversation with Professor Three, I recommend that you do the following.
Take personal responsibility for not knowing what was expected of you. I am suggesting that you say something that includes the words "I failed to understand..." in a way that indicates you've reflected long and hard about the role you played in things going sideways. I am not suggesting that you grovel. I recommend that you be ready to answer the question "Why didn't you know that you were expected to provide synthesis and analysis?" Make an affirmative argument why you should be allowed to take your exams again. You are a historian who has contributions to make to the profession. You have been trained to prepare for and to pass qualifying exams--and you will prove it when given the opportunity to do so. Treat Professor Three's approval independently from the other two committee members. (Do not use the approval of One and Two as a reason.) Briefly outline your plan for preparing for taking your quals (have additional detail ready upon request, but don't over do it). Be ready for Professor Three to ask you a quals-type question during the conversation. Prepare for this possibility by re-reading your written responses and by thinking through the questions that gave you the greatest difficulty during the oral exam. When your conversation with Professor Three ends, look him right in the eye and thank him for his time.  When you get the okay to retake your quals, make sure you know exactly what you need to do to dot the i's and cross the t's--paperwork, scheduling, and everything else that comes to mind. You don't need to do it all right after you get the okay, but you should do it soon. If possible, see if you can get one or two people to sandbox the conversation with Three. Treat the exercise like the real thing.
@serenade, do all you can to put all of your other concerns out of your mind until you have this conversation with Professor Three. Visualize yourself having a positive experience with him. You will be poised, you will be knowledgeable, you will be professional. You are going to show Three that you just had an off moment.  Imagine the conversation going well and getting the answer you want. 

I think it's more important that you have a couple of years' worth of experience in 1 lab, and that you have demonstrated some independence and acquired good (field-appropriate) skills in the process. Your research doesn't have to be ground-breaking or super-trendy: you aren't really evaluated on the kind of research you do, just how well you do it.