scientific

Writing the Statement of Purpose is hard. It's supposed to be. It is a synthesis of years of experience and intellectual development, but, depending on your program, it is also a very purpose-driven document. It forces you to think clearly about why you want to take this next step, and how best to communicate that vision to different stakeholders. The Masters of Public Policy was my program of choice, and I can't think of better preparation.
Before the process I considered myself a strong writer; my personal Bible is Strunk and White, and my work has performed well in the professional contexts it has been tested. Still, the Statement of Purpose is hard.  So, I thought I might offer a few pieces of advice. They may not be helpful, but they're what I wish someone would have told me. Disclaimer: I realize the hard sciences and research-driven SOPs have specific research requirements. While my SOP didn't require that, I'd venture to guess the creative processes are still similar. 
1. If you feel like your first drafts are "perfect", you're doing it wrong. It's relatively easy to string together a narrative and slapdash a philosophy into a few relatively coherent paragraphs (or pages, as the prompt may be). You're applying to graduate school. Everyone can do that. Play with structure, from narrative to thesis driven, always understanding writing as the aligning of audience and purpose. Figure out what works best for you and why it works best. What are the weaknesses you are compensating for, the strengths you are accentuating, and how can you do that with a "show" rather than "tell" execution? How can you set a tone? How can you be different while still being you? These are the questions behind the white page and blinking cursor, and by answering them through writing exercises or more "informal" writing sessions (I prefer pen and paper), you can begin to create a fully functioning draft. 
2. Give yourself time to sit on a "fully functioning" draft for two weeks before doing anything with it. I'm terrible with time management, so the first school I applied to also happened to have the most worked-over, crafted SOP. By being able to shelve it and come back with fresh eyes, I could do a re-write as opposed to a revise, emphasizing certain parts and cutting others. Once I felt comfortable with this document, I started sharing it among my network of LOR writers, peers I admire, etc., which leads me to...
3. Listen to all of your advice, but also none of it. Everyone who has a note is pointing something out that isn't working, even if their identification is off or their diagnosis doesn't work. So be open to potential changes. That said, if you're taking the road less traveled and are truly being a little original, a little novel, a little -- dare I say -- interesting, some people will hate it. One of the people I admire most said of my final draft something along the lines of "It's well written, but it's certainly not what I would have written." At the time it felt like a slight (or a huge blow), but I've grown to appreciate the sentiment. Only one person really understands your Statement of Purpose, so while constantly looking for a better execution is a virtue, being confident in your basic construction is essential. Unfortunately, you're still an academic, which means...
4. You're probably going to hate your SOP by the time you send it out. It's never going to be a perfect distillation of your potential as a graduate student or professional in your field. It's never going to talk the adcomms into admitting you. It's never the all-powerful document we make it out to be in our minds when we are obsessing over dependent clause construction. Still, it's the one-thing (outside of maybe the GRE) you can really control heading into admissions, which makes it a lightning rod for doubt and self-loathing. So, unless your mental health is much better than mine, you're pretty much destined to hate your SOP until...
5. When you finally know where you're going to go, take a look at the SOP you wrote. Most people tell you to tailor your SOP to the school, and while I agree with this sentiment wholeheartedly, I also felt it was important to be honest about my study and career aspirations, even if they didn't align perfectly with the school. That's not strategery out of the "How to Write Your Way Into Grad School" game plan, but at the end of the day it led me to a school with a great fit that also happens to be Top 5 in my field. Also, I'm surprised to report, outside of one typo, one misplaced however, and one flawed introductory clause, it was a document I can be proud of. 
Good luck, and remember. It's supposed to be hard. 

Regarding the textbook: This is a class project. You're right that the situation is complicated so there's no easy way to put this in your CV. I don't think it fits in the publications section. I also do not think this counts as peer-reviewed. I think if you want to include this in your CV, you would have to be a little creative. How much other science writing do you do? If you blog about science or have done other things you might group together as "outreach" or "science communication" or "science education" then you could include this project with the other stuff. Otherwise, if you already have a section on service/leadership/volunteering, then maybe mention it there. Alternatively, if you have a section on projects, you could list this here too, after any research projects you have.
Note: This type of entry is good to have in a CV at the applying to grad school level. But once you are a grad student, I would remove this entry. I don't think it really belongs in an academic CV. It's normal to reflect on your CV and cull old/irrelevant material at each stage of your career. 
Note #2: If you choose to not put this in your CV now, you should definitely write about it in the your SOP. I personally think this is a better place for this entry than your CV, but it's your choice.
Regarding the poster presentation, yes, include it in your poster presentations. But it depends on what you have there so far. If you have like 3 or fewer entries including this 3rd author one, then keep it. Otherwise, I would not include it since having 3 first author posters + 1 3rd author poster is not very different than just 3 first-author posters. Adding that 3rd author poster makes it look like you are trying to CV-pad. Similar to my above note, if you do include this 3rd author poster for now, eventually you will reach a point where you have many first author posters, and there's no longer a need to include non-first author posters. And then later on, you will probably want to limit the number of posters to just 4 or 5 instead of every single poster.

I lived in Davis for a few years. There are venues, events, and campus groups that are geared toward meeting others in the LGBT community. It's an affluent, bigger little college town.

I went straight to PhD but that was mostly because I got into where I wanted to go first try. If you think your GPA will prevent you from getting into the program of your choice, maybe a master's is fine. I'm in a top program for my field (neuro) and no one in my program that I know did a master's first, though many teched for a while. I would say in general, Master's are not required at all for US PhDs. What are your dream schools/programs by the way?

If you have a few not-so-hot grades, you should definitely "touch upon/explain some of the weaker aspects...without directly addressing them".  Adcoms (chemistry faculty) will be interested in hearing about your growth as a chemist.  If you talk exclusively about your strengths (the way a candidate with a 3.9 would), you appear to lack self-awareness.  If you dwell on your weaknesses, you can't effectively sell yourself and your accomplishments.  So, find that middle ground.  Good luck!
Oh, but don't forget to emphasize "fit" (e.g. profs whose research interests you, how your previous research experience complements a couple of projects).  Decisions can hinge on fit.  You might want to contact a couple of profs as well.   

You are not being overly ambitious. You have at least some chance at every one of those schools. Seize the opportunity and see what comes of it. You need to cover all your bases though. You have some very hot and very cold parts of your application. Your GPA is a problem, the ranking of your undergrad institution is a problem, and your time out of school could be considered a problem. On the other hand, you have great research experience and results. 
You need exceptional LORs to get into the schools you have listed. You might get them. You might not. You won't know because most professors don't share letters with you. If you have any doubt about any of them ask "can you write me a strong recommendation" before you put them down on the app. 
With the risks inherent in your application, I recommend casting a wide net. The schools you have listed are ranked between 6 and 41 on US News and World Report. That's a pretty good spread. I recommend adding one more school ranked 40 or below for security purposes. Vanderbilt, Boston College, Colorado State, USC, Arizona State, UC Riverside, and Notre Dame are all respected programs where you might have high odds of admission. 
With a wide net of top ranked schools and good but easier to get into schools, you should at least get in somewhere. 
Don't let money blind you into mortgaging your future. With GRE submission fees and application fees, you can estimate around $100 for each application. But what's $500 or even $1500 in the grand scheme of the rest of your life? Be parted from the money and be thankful for the opportunity to have invested it in your future. In my experience, I applied to 8 programs with so far only 1 acceptance and 2 I haven't heard from. The one I got accepted into was actually ranked in the middle of all the schools I applied to. Putting my finger into a lot of different pots was definitely worth it. I recommend that you apply to at least as many schools as I did. 
Finally, I'll say that working in industry for a while is unlikely to significantly increase the strength of your application and is likely to make your letter writers slowly forget their fond memories of you. With your background and experience, your ambition will be rewarded with an acceptance somewhere. I recommend that you apply for 2017, cast a wide net, hope for the best, have somewhere you can get in for sure, and start researching schools. 
Go through the faculty pages of every school in the Top 25 and see who has multiple faculty doing research that you think is exceptionally interesting and impactful. Apply to those schools. Do the same thing for at least a handful of schools ranked 25-60 to select your safety schools. 
Also skim read the past year of JACS and note who is doing really cool research. 

Your GPA is decent, not great, but high enough to get you past most cutoffs (don't listen to Fun_Cookie). You have good research experience, which will help a lot especially if you get strong LORs. I don't think anybody cares that you didn't stick with a single lab in undergrad, it's the best time to explore different fields to see what it is you want to do. You are looking at prestigious schools, which does mean you're going to face a bit of an uphill battle. If I was in your shoes, I'd hedge my bets and try for a few of the schools on your dream list as well as funded MS programs at lower tier universities because a good record during a MS does help. I would definitely talk to professors you did research under at the Ivy universities, assuming you are interested in the program and what they do.

3.3? Please you would not survive the first week of grad school.

It will really come down to how well you can sell yourself to the adcomms at these institutes (i.e. your SoP) and the strength the LoRs submitted on your behalf. Take your GRE, write a strong SoP and apply to any place that has interesting research being conducted (i.e. 3-5 PIs/institute). Also if you are in the midwest why don't you look at Ohio State IBSG and the IUPUI IBMG programs?

You've got a pretty good shot at a lot of these schools. Your academic stats are eh, but your research is a lot more impressive than average, which is the most important part of your application. I think you've got a nice range of schools that you're applying to already, only widen your range if you feel like you want to do so.
If you're applying for the 2019 cycle (?), I would try to get more research experience in your desired field. This would help 1.) show your continued interest and abilities in your field and 2.) help you build connections that will turn into good LoRs. That being said your application is decent as it is.

The best way to figure out things like this is to ask grad students in the department.  Not even just grad students in the lab in question, but some people in other labs might have heard rumors.
Some telltale signs that a PI is in a rough spot funding-wise -- if he's only accepting students with fellowships, if the students in his lab without fellowships are forced to teach far more than the departmental minimum, if he spends far more time than normal writing grants instead of attending conferences.  Consider asking students in his lab how life is for grad students without a fellowship.