BabyScientist

I agree with @mcfc2018. The goal for you in emailing a PI is getting to know them/their research/their opinions of the program. If it goes well enough, you might build a relationship with them, and they might ask you directly about gpa/shortcomings, but don't bank on it.

Neurodegeneration

Definitely not bad form, I'd encourage it. Get an idea of if the people you want to work with are good people and if they're even taking students. Reach out and express your interest in their work and that you're applying and would love to hear more about their work/the program. I had a few phone calls with faculty of interest. EDIT: this won't necessarily help your chance at admission, but is more for you to know what you're getting yourself into before you apply.

Definitely normal to contact PIs. I don't know if any places to get examples of the 2, but an SOP should be more based on your research interests and experiences that lead you to want to pursue a PhD, and why you want a PhD. A PS is more of a who are you and what brought you here, academically relevant or otherwise. SOP is more about your academic life and a PS is more about your whole life.

I mean honestly it's hard to say, but that's just been my impression (the "tiers"). What I did was just think of areas where I'd like to live and look up what schools are there. If they had at least 3 faculty I thought I'd like to work with, I applied.

Why not do your best to get things together now and see how the timing works out?

Not sure why you're so hard on yourself... A 3.6 major GPA and 3.75 overall GPA is great. No one cares much about GRE but your scores there are fine. 6 publications is a lot - they don't expect you to have any, so they definitely don't expect first authorships. Your chances will largely depend on the strength of your LORs and SOP, but on paper you're a great applicant for most of those schools. I'd say UNC and Wisconsin are in the "reasonable" category, probably Vanderbilt too, but I don't know much about them. I'd call Washington and Chicago "upper reasonable" , but it all depends on those LORs and SOP. My GPA was lower than yours but everything else was about the same and I got into schools at least UChicago/Washington tier.

I interviewed at BU and got the vibe that there are a lot of politics between the departments. In my current program, 3 of us interviewed for 3 different programs there and got weird vibes from them.

I think you'll get better input from the physical sciences - astronomy page or the applied sciences - engineering page.

In the end, no one will ask which program you got your degree from, just which school. Any degree in neuroscience from BU will, later on, come with the same prestige. It'll matter more what faculty you work with. BU has 3 separate neuroscience programs (also behavioral neuro), which is just weird.

Contacting PIs in advance wouldn't increase your chance of acceptance, unless you got really lucky and emailed someone on the adcomm. I recommend sending emails - it'll help you get a better idea of if you want to apply to those schools. If your faculty of interest aren't taking students, no reason to apply. Considering your experience, you have good odds at interview offers at a bunch of those schools. It'll depend on SOP and LORs now.

Hm, you're producing the data? How about analysis? Sounds like grounds for authorship... Have you expressed to your PI that you want to get on papers? It's not a big deal for graduate admission, more so just an ethical thing..

I think that's a solid list. No publications? That can be excused since you worked industry. It'll depend on strength of LORs and SOP. Good luck!

I've heard that mentioning during interviews that you're significant other goes to the school and you are absolutely going to attend if admitted helps your chances. They like admitting people they know will accept so they don't waste slots. I don't think you should mention it in SOPs though. They won't offer you an interview because of it, they'll offer you an interview only if you're qualified.

I have nothing concrete, but I met someone during an interview who had been working in Italy and she said they flew her over. She had to pack all her interviews into a month though to limit how many flights had to happen.

Remember that everyone coming in has a different background. There's no shame in asking for help - definitely better to ask for help than to mess something up because you weren't sure. Things fail all the time in lab, what they'll care about is how you handle it. The PI will know that what matters more is how you handle yourself - new techniques are easy to teach, human behavior... not so much.

The actual content of what you'll be learning in each program varies dramatically, though. Generally you apply for the degree that will teach you the content you need to perform the research you're interested in. If you want to learn about genetics, do a genetics program. If you wanted to be in a neuroscience lab, usually you can join labs from different departments and still be getting a certain degree. Clinical psychology is the most random of the three, as it gives you a completely different set of skills, but if that's another interest you want the potential to pursue, that's fair. I'm just trying to understand how you chose genetics vs neurobiology at those schools. Generally, I think your application is strong enough. Your GPA just might prevent you from getting through at places like Harvard or Caltech. It's all on SOP and LORs.

Those are very different programs. Clinical psychology, neuroscience, genetics.

Women, not as much, but minority, sort of. More funding options are open to minorities and funding agencies like to fund minorities, which means universities like to accept minorities because they're more likely to get funded by outside sources.

I'm happy to read it

Ask letter writers a few months before the apps are due. If you tell them too far in advance, they'll forget. I suggest asking after apps open, in case they want to do it right away. Make sure to follow up a couple weeks before apps are due. Don't expect them to do them in a timely manner. Shouldn't matter if you spell them out. If you have the space, go for it, otherwise, they know their own program's name. I recommend making it a CV. Consider what's most important to them and order your sections that way. Mine was: education, research experience, publications and abstracts, other experience.

Not at all!

I'm happy to help! You also might want to consider letters of rec as a possible cause of last year's outcome. One bad line in one letter of rec is enough to blacklist someone.

Like I said, they don't scrutinize every course you've taken, and they won't scrutinize courseloads. If taking fewer courses will help you do better, then do it.

Your GPA showing improvement over time should help. I suggest having people review your SOP, it's hard to judge your own writing about yourself. I'm happy to help with this if you want. No one can make a list for you - we don't know your interests. What you should do is look for faculty you're interested in working with and apply to the schools that have at least 3 faculty you're excited about. I'm happy to review such a list once you've made one.