So for the most part I've already decided which programs to pick at each school (mostly neuroscience programs) and I also have a list of potential advisors that fit my specific research interest in MRI and EEG methods in clinical populations. Do you think there's any disadvantages to contacting them before I have an interview, for example, will they get annoyed or will they just not respond?
Before the interview they may just not respond. Most PIs just tend to be very busy and if they're not on the admissions committee they aren't gonna say much pre-interview. Post-interview (really post acceptance), they may be more inclined to answer your questions. This is all based on my experiences so others may have other things to say.
I didn't really see a difference in approaching faculty at various sized institutes. Just be polite and concise. Now if the PI happens to be really high up the academic food chain (think academic administration), they may be a little hard to reach so reaching out to the program coordinator, secretary, etc. may be a bit easier.
I think that contacting potential PIs pre-interview is too early. The proper procedure is that you suggest them as possible interviewers to the coordinator when you interview at the program. Many programs solicit thus, and it's acceptable to ask if you can meet x, y, and z when you interview. Thus, you then meet potential PIs at interview or second look.
Nothing bad will likely happen to you if you do contact them.