Yes, Scripps has been accepting trans applicants since 2014 Scripps Approves Trans-Inclusive Admissions Policy - The Student Life
The Queer Resource Center serves the whole consortium and is good source of information on the nuances of housing, etc. Scripps College - Queer Resource Center at The Claremont Colleges
I’m not an expert on UMich, but my understanding was that they met documented need for family incomes under 60K. Probably someone on the UMich forum could help clarify why your NPC isn’t looking favorable.
Rochester is a great school. It’s true that it’s pretty cold there, but it’s a terrific place for students who are also musicians, and excellent academically for your interests. I’d think it could be worth applying if the NPC looks good, even if it’s not at the top of your list at the moment. URoch has a large international student population (more than 25% of undergrads), so it’s actually a bit more diverse than the domestic-student demographics would suggest, and even those numbers aren’t bad.
If you’re interested in the urban Boston schools, both BU and Northeastern could be worth considering. NEU doesn’t have CogSci per se, but they have blended majors that can be customized in that direction, especially if you’re interested in the computer science piece (CS+Behavioral Neuroscience, CS+Cognitive Psych, CS+Linguistics) or a design focus (Behavioral Neuroscience + Design). Tufts would be another reach but less so than Rice, and it could be a good fit. (They have both Cognitive & Brain Science, and an interesting Engineering Psychology major.) Nice balance of a self-contained campus with great access to the city, and definitely good in terms of LGBTQ-friendliness.
If you like Vassar, you may also like Skidmore and Connecticut College. They don’t have the robust CogSci department that Vassar has, which is unusual, but they have similar vibes and meet full need, and you could probably find a combination of coursework that you would like.
Consider other women’s colleges too. Mt. Holyoke could be a great target, and is part of the MA 5-college consortium. Mount Holyoke will now accept applications from transgender women MoHo has a Neuroscience & Behavior major, and the Consortium has a Cognitive Neuroscience certificate program that’s open to all five colleges.
Test scores have become less important generally, but they might be a little more important for you than the average applicant, because rigor is harder to prove on your transcript. The 800 is impressive, and a 650 isn’t bad at all, especially considering that most of your formal education hasn’t been in English (unless I’m misunderstanding). What level of math will you be in next year? You’re a strong applicant, but a little atypical which makes results even harder to predict than normal - you’ll do best at schools that take a close look at your individual situation and don’t just filter for a high weighted GPA. Strong teacher recommendations will be important, as well as a strong counselor recommendation that puts your transcript in context and gives more information about the rigor of your HS program.