BabyScientist

What this person said. Evaluate which school has the most faculty you'd want to work with. Talk to your top 1 or 2 favorite faculty across the schools, see if they are taking students, and if you vibe with them.

I didn't really study for any of my interviews after my first one. For my first interview I read at least 1 paper for each professor I was meeting with and took all these notes and wrote down questions, etc, and none of it came up in an entire day of interviews. I came up with completely different questions on the spot, and they told me about their research themselves. Didn't study at all after that. I recommend just knowing generally what they study (ie memory in drosophila or mouse models of Parkinsons). During the interview, they'll tell you about their work, and as they talk you will ask questions that come to mind or make connections between their work and yours, but the more important questions you ask wont be about science, they'll be about the grad program, their lab dynamics, their mentorship style, etc.

Post your stats!

I would say there are no safeties for grad school. Yes, UW is very competitive, but so are all the other schools. And UCSD is also more competitive than you'd think. It's not about the school it's the specific department. I'd swap UCSD and Princeton on your lists if anything. That being said, assuming you have decent letters of rec and write a good SOP, you stand a good chance at any of the schools you listed (if you're international though, your odds go down a lot)

I had a worse GPA but more publications, and I think the Duke, BU, WashU tier is about right (I got into BU, didn't apply to the others). It'll definitely depend on your statement of purpose and letters of rec, but you can include the paper that isn't published yet on your CV and say "manuscript in preparation" and it counts.

I interviewed 3 years ago XD

Unlikely if you weren't even offered an interview. If you were interviewed and waitlisted it likely would've made the difference, but unlikely if you weren't interviewed.

Potential advisors is key. Of course you can't know who you'll end up with, but which program has the most faculty you want to work with? Which program gave you the best vibes? I'd recommend emailing faculty you're most interested in at each program you're considering and asking for a meeting/call, and talk to them about your deciding process.

This is exactly the answer I'd give (current student). Focus on the lab, not the institution. It will matter wayyyy more who you worked with/what you accomplished than where you did it. Choose faculty who will be good mentors and who have the resources for you to do good science. Doesn't matter which institution they're at, matters what you can do in the lab.

What can you do to get into the 1 school you're applying to where multiple faculty have told the admissions committee they support you? Don't be an ass at the interview. Seriously. That's it.

Didn't even catch that... NIH postbac program doesn't have an admissions fee. Not sure about others, but seems silly for them to charge you if they're also going to pay you...

Your plan sounds solid to me... I was a RA and am very glad I did it over a postbacc program. I guess in part it depends on the lab you work in, but I published as an RA, made great connections, and saved a ton of money. I had my own projects, and helped some others with their's, but I wasn't responsible for everyone's stuff. For the argument that postbacc programs are designed to make continuing education easier... It can be the same way as an RA if you make it that way. My lab knew I wanted to go to grad school so they set me up with opportunities to do so: publishing papers, presenting posters at conferences, etc. I was fully expected to leave and start grad school. For the argument that you wouldn't have time for stuff in the morning and evening... Again, depends on you and the lab. Many labs pay RAs hourly, so I'd argue postbaccs end up getting overworked because they have a set salary. In my RA lab I was encouraged to work as much as I needed to to get my stuff done, but not too much more, so it varied by week. Again, I wasn't responsible for other people's projects. If I busted my butt it was for my project or projects I was sharing with someone else. Postbacc programs pay less, and often have restrictions on if you're allowed to have additional employment to offset the living expenses. I felt like I was rolling in the dough when I was an RA. Honestly, I work with a lot of postbaccs now and what they do is fundamentally no different than what I did as an RA. There's no wrong path, just a different path. Do you.

The department you're in matters mostly only in the structure of your program. The training you get is mostly from your lab, so if you have access to your labs of interest, the program doesn't matter as much.

I think a second masters would serve you less than a research position if you ultimately want a PhD. Your application is fine for a PhD, depending on your LORs and SOP, but not for programs of that caliber. A research associate position would give you opportunities for publication that will certainly help.

I've heard of people having a post doc write the letter and the PI cosigns it. It's like the PI saying I don't know this kid but I trust the judgment of the person who wrote this. If you feel he could write a good letter after knowing you a short time, couldn't hurt.