Thanks for the input, everyone. The thing is that this program is a little differently structured than most in terms of admissions. Only one of the PIs that I emailed was part of the admissions process. She interviewed me during my interview weekend. We really hit it off and connected during the interview. (We even hugged at the end of it!) The other PIs had no part of the admissions process at all; the adcom had no idea that I was in contact with them, other than that I had requested to meet with them during my visit, but they were unavailable. I think one of the reasons I was placed on the waitlist was because I wasn't able to meet with very many faculty members that shared my research interests during my visit, and thus, it could appear that I'm not the best "fit," although I certainly am. The faculty I requested were simply unavailable to meet with me.
Two of the faculty I emailed are not "core" Neuroscience department faculty, are therefore not on the admissions committee, and almost certainly didn't discuss me with the adcom. Only one remaining PI had a small possibility of doing so.
By emailing these PIs and asking them to write a short email to the adcom, I was hoping to provide more evidence of my fit in the program. I hope that I haven't, as you guys have suggested, hurt my chances by doing so.