MathCat

You could ask but I doubt you'd get a satisfying answer. This seems like a totally generic reply so you might just respond with a 'thank you'. You don't need to feel obligated to continue the conversation, this reply doesn't really suggest that he is interested in that. (But of course if you actually have questions about the program, he has indicated that he is willing to answer them. Just make sure they're not clearly answered already on the department website.) Otherwise, I'd leave this alone and would at most follow up after submitting the application to let him know that you did. 

I would include all of them at this stage in your career.

Wow.
1) You do belong. I study belonging and the construction of inclusion and exclusion. You applied there, you got in. Make it home. If you feel you don't belong because of your background, then communicate your background to peers so that they know. If you feel you don't belong because you still struggle economically, well, I think you represent most grad students PM if you want to talk further.
2) I think you should talk. If you don't feel comfortable talking to your advisor, talk to the old one or the DGS. The DGS is here for this type of things. He/She should meet with you and talk to the professor safeguarding your privacy. Maybe they drop the subject in a meeting. But it is clear that professors in your department should be more sensitive, especially since clearly they are open to "traditionally underrepresented students" since they admitted you. You displayed a calm attitude and you differentiate the different sides of this story ("she was not in the admission process" etc). So I think you could have a professional conversation about this.
3) Look for a mentor. Clearly, this advisor will not work as your mentor because you need someone who understands your background and helps you build from it, not in spite of it.
All the best!

Assuming that this is at least partly about my post, and I wasn't trying to cast personal blame on you. I don't know you or what you do in your daily life, but from all I know about you from this board I would have no reason to suspect that are anything but a good contributing member of your academic community. But I still find the content of your post very frustrating, and that was the point of my post. I fully understand that someone low in the hierarchy of their academic institution and who depends on the evaluation of other faculty members may not want to criticize them or point out potential problems with their behavior. But while young male faculty members work their way toward tenure, other women aren't getting the opportunities that they deserve, as undergraduates, as graduate students, as postdocs, as young faculty, at every stage, really. Old tenured men can't be the only ones who can help, or we will never fix anything. I find that frustrating, but I do apologize if you thought my words were explicitly directed at you. They weren't. The problem is much bigger than that, and that's where they were aimed. 

Consciously or not, the male faculty are more worried about their reputation than the education and opportunities available to their female students. They have cut off opportunities for women that could possibly be perceived as inappropriate, but they still allow those same opportunities to the men and they have done nothing to offer alternative opportunities to the women. Saying that they "aren't doing it by direct choice" is taking away their agency in this, and it is a choice they are making. Saying that the problem is facing academia as a whole is of course correct, but absolves these professors of having to take any responsibility, and I object to that. The way you address these problems is not (only) by decreeing change from above, or leaving it to the affected (and hence weakest) party in this interaction to fix. It is by taking action as an individual where you can, and speaking up about these injustices, especially as a man (or any other privileged group member). I don't think you fully appreciate how much more impact it has when a man points out an inequality than when a woman does. There are so many small ways you (as a male faculty member) can help and places to speak up, and you need to be an ally, not just say it's a bigger problem than any individual can solve. It is because every individual shirks responsibility that we, as a whole, don't seem to be able to solve the problem.

You know what?  Because you can't do anything and you did your best, you need to repeat after me:
Fuck that guy.  Fuck that class.  Fuck that rotation.
I know we're supposed to use professional language, but sometimes you just have to drop a few F bombs.  There is nothing you can do to change it other than move on.  Work hard to do well in your other classes, choose a different rotation.  Identify what you could have changed and make it a point to work on those things in the future.  Do you need to learn better study habits?  Do you need more of a work-lab balance?  One failure doesn't constitute an entire career of failure.

Assuming that you can afford $70, I think the money is a good investment for more opportunities. 
The time spent altering your SOP could be more costly. Does it mean you have less time to optimize your other applications? If you do have the time to do this SOP change and give everything else full effort, I'd say go for it. If it will remove time from other applications, then you have to decide at some point whether the risk is worth the reward.
I would lean more towards applying though because I think it's more likely that one underestimates themselves than overestimates. However, I don't know your actual scores and GPA. Maybe you can get better advice from someone who knows you personally (e.g. your letter writers).

I'm from Canada where we must do a Masters before a PhD (2 year MSc, 3-4 year PhD). But even if it was not required as part of the degree path, I like doing a Masters first because I don't want to commit to 5 years in research without a way to get out in 1 or 2 years in case I didn't like it.
Also, if I was in a place where I had to choose between low rank PhD or Masters->Apply for higher rank PhD, I would choose the Masters first. If I couldn't afford the Masters then I would try to find work or do something non-academic and re-evaluate when I was in a position to apply for grad school again. This depends on your career goals though. But given the toughness of the academic job market, I would rather pick a non-academic career path than enter a PhD program that isn't in the top tier. (Not that graduating from a top tier guarantees anything, but my personal view is that prospects for job satisfaction are too low without a top tier PhD).

I'll preface this by saying I'm not in statistics. Getting a C in an upper division math course could definitely hurt you. Given that it's linear algebra, it's an even bigger deal: I know linear algebra is very important for (most, anyway) statistics programs. If you got a C in abstract algebra, it would probably not hurt you anywhere near as much as a C in linear algebra. I know you say it's because of proofs and you won't be doing proofs in the masters program, but I'm not sure how much that would matter to an adcomm. You would somehow have to explain that it's just the proofs part giving you difficulty, and I think this would just come off as a weak excuse at best. So I would recommend taking it in the spring if you are certain you will not do very well.

I have read many of your posts, and I am fully aware of your tendency to post vague one-liners (often questions) that you seem to think are so obvious that everyone should agree (alongside those more thoughtful posts that I agree you do post as well). And if you pay close attention, you will notice that I never respond to those. I will stick to that, because I have never found that those discussions lead to anything useful. All I will say is that despite being a moderator, I am entitled to -- and am posting here -- my own opinions. These are based on my own actual experiences, as my signatures always states, and unfortunately I have quite a few of them. I do think that micro-aggression is an appropriate term here, since this is part of a larger pattern of behavior that women deal with in the workplace, but that is independent of, and does not preclude, a low-level attempt to solve this problem by talking to whoever the relevant individuals are, and not attempting to solve the larger problem. I explicitly said as much in my post, and the OP or anyone else can take that part and disagree with the other. You may disagree with my opinions, and that's perfectly fine, too. But your post above attributes all kinds of ill intentions to me that I don't think even deserve a serious rebuttal. If you truly believe that I have such sinister intentions, or alternatively that I am entirely oblivious, then we are too far apart from one another to have a real conversation. And if not, then the entire discussion needs be reframed. As such, I have no intention of engaging any further. All you are doing is hijacking the OP's thread and taking it in a direction that I don't find particularly helpful. The time I spend on this forum is volunteered and limited, and I'd rather spend it helping others as best I can instead of participating in this debate whose purpose now seems to be you admonishing me for apparently not behaving as you would like.    

I'll preface this by saying I'm not in statistics. Getting a C in an upper division math course could definitely hurt you. Given that it's linear algebra, it's an even bigger deal: I know linear algebra is very important for (most, anyway) statistics programs. If you got a C in abstract algebra, it would probably not hurt you anywhere near as much as a C in linear algebra. I know you say it's because of proofs and you won't be doing proofs in the masters program, but I'm not sure how much that would matter to an adcomm. You would somehow have to explain that it's just the proofs part giving you difficulty, and I think this would just come off as a weak excuse at best. So I would recommend taking it in the spring if you are certain you will not do very well.

I'll preface this by saying I'm not in statistics. Getting a C in an upper division math course could definitely hurt you. Given that it's linear algebra, it's an even bigger deal: I know linear algebra is very important for (most, anyway) statistics programs. If you got a C in abstract algebra, it would probably not hurt you anywhere near as much as a C in linear algebra. I know you say it's because of proofs and you won't be doing proofs in the masters program, but I'm not sure how much that would matter to an adcomm. You would somehow have to explain that it's just the proofs part giving you difficulty, and I think this would just come off as a weak excuse at best. So I would recommend taking it in the spring if you are certain you will not do very well.

Yeah, you are definitely not the first or only one who something like this has happened to. It's unfortunately more common than it should be. It's very unfortunate that this male student doesn't sound like someone who will help. The best ways I know of combating such a situation involve recruiting a man who can point out microagressions and unequal treatment in a way that women who are a part of the situation often cannot. @knp gave you some very good advice, but I would suspect that in this case it may be very difficult to solve the problem, since you say that all of the professors are male and the male student likely won't help. Maybe you can still identify an ally among the professors, but you should be careful about that. You don't want to be perceived as complaining or imagining injustices (even if they are actually real!); this is why having a male ally could be so important. If you did want to take this further, there may be venues you could bring this up in (the ombudsperson comes to mind), but you'll never be able to get someone to socialize with you who doesn't want to. But if this leads to favoritism in the workplace, that's something you can try to address. 
 
This is definitely not petty. It's one more micro-agression in a world of many small and large gestures that signal to women that they aren't as wanted, aren't as good, aren't as likely to succeed. It's understandably incredibly frustrating. I don't know if we can help, but you are not alone. At least know that. 

I know at least one person who got it in their first year of their graduate program. My advice is to apply in every year that you are eligible, it will make later years easier and you might get good feedback to strengthen your application next time around.

Come talk to me next time:
1: You get woken up by barking because your dog saw a squirrel / the garbage man / his own tail.
2: You have to pick up feces with a pooper scooper or a plastic bag.
3: You can't stay at school for more than 8 hours because you need to let your dog out.
4: You notice a sock, a chunk of a dining room chair, or a cardboard box disemboweled on the living room floor.
5: Your vacation becomes a source of stress, since you can't leave a dog at home for very long without someone coming to check on it or let it outside.
6: You have to potty train a dog, since unlike using a litterbox, having to request to be let outside every time it needs to "go" is not a natural instinct.
Now, of course I made this post in jest... I love dogs, and had both growing up. However, as a grad student, having a cat is generally more feasible. This is not to imply there aren't downsides to cats - this coming from someone who just had to fork over $300 for a vet bill (though that isn't cat-specific), but dogs as a whole require more attention.

I will also say that it is very likely that your courses will not transfer. If you want to go to a new school, you're likely going to start over again, at year one.
I also want to second @Butterfly_effect's point about the importance of mentorship and research fit over research fit/passion. I always say that these two things are important for happiness and productivity in grad school, however, it is much easier to change your research interests than your PI's mentorship style and lab culture. If you find a good PI and a good lab at a school/department that is a good fit for you, I'd hang on as best I could! 
From an outsider's point of view, it sounds to me that you are focussing too much on the little differences in research topics. To me, it sounds like your "dream project" and what your lab does is very similar, just not exactly what you were hoping for. Since I don't know the terminology of your field, I'd use an analogy. To me, it sounds like your ideal grad school project is to study the best pastry making methods because you want to make apple pies. However, the lab is working on making Beef Wellington, but part of a good Beef Wellington is a nice pastry crust, so they are working on developing pastry methods too! 
My advice for new and prospective graduate students is to avoid framing your research interests as a specific topic or research question. Instead, when picking labs in grad school, think about what are the things you want to learn by the time you leave. Grad school is a training ground---I think of it as an "incubator" for us to develop into independent scientists. So, I don't really care that much whether I work on making apple pies, cherry turnovers, or Beef Wellington. My goal is to develop good pastry making skills so that I can go out there and become an independent researcher.
I also think flexible research interests is good for you personally and good for science overall. It's good for you personally because you will be able to "follow the money" and do whatever work that is getting funded. Having narrow interests in grad school means that you might have to adjust to this during postdocs and later in your career. That is, you might just get lucky and have the perfect fit project in grad school, but that's not always going to be the case later in life, so I wouldn't stress about it now. I also think it's good for science and academia in general to be flexible. If every scientist decided on research interests for life in grad school, our field won't be able to adapt to new discoveries and work on whatever is at the forefront of knowledge at a given time. 
Okay, so here is my suggestion on future steps:
1. Don't do anything now. You've only been here for a few months. You gain almost nothing from leaving the program right now so give it some more time. Do not contact the schools that did not accept you to see if they would reconsider you. They didn't accept you during the regular season, and they are unlikely to somehow change their mind. If there were schools that accepted you but you declined, then maybe there is a chance. 
2. After 1 academic year in the program (e.g. the summer), re-evaluate how you feel about the research fit and the city and the lab fit etc. I understand your ethical concerns about staying longer knowing that you will leave, but I don't think it's a concern if you fully commit to keeping an open mind until next summer. No one will expect you to know within a few months whether or not you will stay. 
3. If you do decide to leave next summer, you should tell your PI right away. This will give you the summertime to figure out the next course of action---whether it's to stay and finish the MS (and whether or not you will still be funded in the 2017-2018 year) or to just leave and take a job while applying for more schools. 

In response to Pink Fuzzy Bunny, I don't think most courses will transfer. At least in neuroscience, it's very rare for a grad school to accept coursework done at another institution. Maybe if you got a master's but even then it might not transfer. 
 
I'm also a bit confused about why you're leaving. The only real complaint I can glean from your statement is that your lab doesn't focus exactly on what you want to do and isn't quite as translational as you want. I'd just like to say that your lab doesn't have to do exactly what you want in order for you to study it (you mention that you could work on B even if most of the lab does A). As long as your PI is supportive of this, I see no reason why this is a detriment. Most grad students end up expanding the scope of the lab's research in some way (otherwise everyone would be doing the exact same thing). I also don't know what you want to do after grad school, but it probably won't be what you do for your dissertation. I wouldn't worry if the project doesn't fit the most narrow definition of your research interest. Personally, I think mentorship and fit in the lab is way more important than the actual research. Most people are more flexible than they realize in terms of what they're 'passionate' about, and indeed this often changes over time as you're exposed to different kinds of research. I guess I'm suggesting you ask yourself what your overall fit is with the program and what your chances are of finding a better fit somewhere else are? You've only been in the program a few months. Are you really sure what you want is to leave?

One last thing: don't forget to take time for self-care too. Find friends, family, etc. who will support you. If things get worse later on, ensure that you take some time to get this support and take care of yourself! 

I know this is a hard time for you. Here's my advice. (Note: I have not experienced this myself but know others who have).
1. It's okay to say that you don't know what's going on with your PI. You are not your PI's personal assistant. You are also not their family member. Like @Sigaba suggested, you should pick a careful statement, practice it and say it to everyone who asks you about it. Something like, "I am not sure what is going on and I hope to find out soon" etc. Also as Sigaba suggested, you don't want to have it over-rehearsed, so feel free to alter your responses and be honest on how you feel with your close friends etc. but for the random people that will just ask you, I think it's okay to have the same 1-2 sentence answer. 
It's good that you are talking to the DGS etc.
2. It's nice for you that you had a really good relationship with your PI. But if your PI is on leave because he was harming other students, be mindful that your experience is different from others. Be very careful to think about your colleagues too---emphasizing how much you liked him could be harmful/dismissive to those did not have good experiences with him. Generally, the worst offenders are very "good" publicly and to certain students and terrible to others. So, just keep in mind that everyone will have different experiences. And that someone can be a very good mentor etc. but terrible in other ways.
However, this is all assuming the worst case scenario. Maybe there's nothing inappropriate about his leave at all. But I'd generally play it safe and follow the advice here.

I agree with the above advice that you shouldn't get involved in whatever circumstances/situation that lead your PI to be on administrative leave. Don't defend your PI---clearly there are many things you don't know and most cases where someone would end up on such a leave stem from some serious misconduct that you didn't know about. You can hurt your own reputation by defending someone who has committed serious offenses. 
Another tricky thing is that sometimes not taking any sides can be considered taking a side. For example, if it turns out that your PI had inappropriate relationships with students, harassed them, etc. then being "neutral" in this sense can reflect poorly on you as well. There is little way for you to win while still being associated with this PI. So, I second the advice to talk to the DGS and look for another advisor. 

By 'top tier Econ School' do you mean that you intend to get a PhD in economics? If so, while your undergrad requires only calculus, you should take several additional classes. I think that at minimum you need at least Calc 1-3 and Linear Algebra. To get into a top program you also probably need Real Analysis (most would say you definitely need it). 
I have a friend who took most of his math at community colleges and then is taking Real Analysis at his university. If he gets an A, he figures it'll legitimize his other classes. I think that's a bit of a risk, but some combination of community college and university classes would probably be ok. I wouldn't take all my math at a community college. That being said, it sounds like you're just talking about taking math classes at other universities. I think that should be fine. But again, you're going to need more math to get into top (PhD) programs.

The situation might be a "wheels within wheels" type of thing that can end up crushing people further down the food chain. Stay as clean and as clear as you can. Keep your ears and eyes open but offer no opinions and form as few conclusions as possible regarding why your POI is on leave.  Stay away from the gossip, even to the point where you remember that you needed to be somewhere else five minutes ago.
If the DGS or the department chair read you in--IMO they shouldn't--and then remind you to keep the conversation in confidence, say "What conversation?"
If such a conversation takes place, understand that you're being trusted and you're also being tested. In that moment, you may need to figure out what kind of a professional academic, if not person, you want to be. If you think there's a certain appeal to knowing where the bodies are buried, understand that there may be a time when you're handed a shovel and a sodden burlap sack.
IRT @fuzzylogician's guidance, there's another possible outcome. The PI is completely exonerated, the PI's relationships and professional stature are untainted, the department wants the PI to stay and the PI does, too. But the PI is now very angry. What then?
 

I think that the answers to your questions don't matter. It's not about him, it's about you. I would schedule a meeting with the Director of Graduate Studies or the Chair of your department ASAP. The question to ask is not what will happen to him, but how they will work to support you during this time when you don't have access to your advisor. Ask to be assigned a secondary advisor, hopefully someone who would be willing to take over in case your advisor doesn't come back. Putting someone on administrative leave and not allowing them access to their students is a drastic move, and would imply that something is seriously wrong, and could take a long time to figure out.* I would guess that this may not end well for your advisor, given that this has happened. Even if he is fully exonerated from whatever the charges are, his reputation has been hurt, and likely also his relations with colleagues. He may not recover, or he may want to move to a new place of employment. (Of course, these are guesses, I have no way of actually knowing what is going on!). Either way, I would suggest that you take steps to protect yourself in case your advisor doesn't come back, or even in case his reputations is so hurt that even if he does survive this, you won't want to be associated with him. 
* Guesses: the two things that come to mind are some inappropriate behavior toward a student or colleague (some kind of harassment or mistreatment) or a problem with academic integrity. But again, these are baseless guesses. If I am on the right track, though, these things can easily take several months to figure out. Official sanction procedures are slow. 

I would send only the second. 14% quant doesn't look good, and a 0.5 difference in AWA is negligible I think - both are good scores anyway.

There's no single answer for this because it will just depend on who you are living with. Normally, many of the things you ask here are discussed with potential roommates before moving in. In an ideal situation, if you are moving into an apartment with people already living there, the current residents will probably want to meet with you and chat to see if 1) you get along and 2) you share similar ideas on things like privacy, food, etc. This is a common way people find roommates. Another way is to find the person you want to be roommates with first (e.g. other students in your program), meet them, determine that you will get along and then look for a place together. So, what I'm saying is that these things should be sorted out before anyone signs any lease or other binding agreement!
For food, a common arrangement is that you only eat your own food, unless a person has indicated something is up for grabs (e.g. maybe they have a made a lot of it and it would go bad otherwise). Typically the refrigerator and pantry would be divided up into areas that are for sharing and areas that are for personal use. Some roommates will go grocery shopping together (and split the bill) so staples like eggs and milk are shared, while other roommates prefer to do everything on their own. 
In almost all circumstances, it would be incredibly rude for a roommate to go into their roommate's bedroom without permission. Even so, it's important to have discussions like I mentioned above when considering moving into a place with roommates. Depending on the apartment, you may not be able to actually lock your bedroom door from both the outside and inside. So, this is why I think it's really important to meet your potential roommates and see if you trust them / feel comfortable with them.
For your last Q, there are other things you should keep in mind when selecting roommates. One big category is the etiquette/agreement on having guests visit (both having friends come hang out and having someone spend the night). Some roommates may have rules on whether or not it's allowed, how often it should happen, whether it's limited to certain days or certain times, and whether both roommates need to agree to it (e.g. if you want to have a party etc.) Other categories of things to be discussed are things like whether pets are allowed, how to divide up the chores/cleaning of common spaces, whether there's quiet hours for the apartment/house, what kind of utilities/services you want (e.g. TV? Internet? phone?) as these costs are generally shared by everyone etc.
And finally, I would say that you shouldn't let others take advantage of you, but it's important to be patient and flexible where reasonable. Living with other people is an adjustment and there will probably be times where your limits will be tested. You may have to make full use of your conflict resolution skills. One thing to keep in mind that sometimes it makes more sense to give the other person the benefit of the doubt at first, and then escalate if necessary since it's easier to escalate than to de-escalate.