Don't underestimate the value of a Pass/Fail curriculum, and of PBL. Columbia and Yale are attractive for many reasons (students, P/F, etc.), but I didn't care for the curriculum at either place. I remember that while I was still at SJC, there were a few students who talked about down-playing the fact that it was their undergraduate institution, since it's quite unusual and a bit difficult to explain to those who know nothing about it. However, I found that most places have heard of SJC--and whether they have or not, they generally think it's fabulous (which, of course, it is) when you tell them about it. So if you're enthusiastic about SJC (and I really, really hope you are, because it is the best place ever and there is nowhere else like it), let it show.
I settled on UCLA because it has a neuroscience faculty that really appeals to me, but its curriculum is by far the most Johnnie-like of any. Once I got in, I withdrew from almost everywhere else. Now that I'm in school I can't imagine studying anywhere else and liking it as much. I was afraid that med school would be a torrent of information stuffed down my throat for me to regurgitate, and that I would be miserable till grad school, when I could actually THINK about things, and ask questions, rather than memorize all the time. But UCLA isn't like that at all, and I'm happier than I could ever have imagined. I wish there was a greater love of inquiry among my classmates--fewer keg parties and more contemplative discussion--but nowhere is perfect. I would definitely say that the students at some other schools were more my style (notably Hopkins, if you disregard the stressed-out streak), but you have to make a decision somehow, and I ultimately decided that curriculum, grading, neuroscience, and location were my deciding factors.
Good luck!