Thanks for the advice, but I feel that my app as a whole is pretty strong (obviously the MCAT score is good for MD/not very good for MD/PhD). I've been working extremely hard for the last four years at a top 20 school doing lots of research, leadership, and teaching, all aimed at being able to pursue academic medicine as a career. The two rejections so far have come from schools that probably just looked at stats very superficially (I'm guessing my MCAT score was probably 95% of the reason for my early rejection, given that I didn't have the chance to make my case with more school-specific essays). There's a lot of depth and strength in my experiences thus far, which I've hopefully been better able to convey in the schools with more extensive secondaries (Duke comes to mind), so hopefully I'll be getting some good interview news soon.
I feel that my app as a whole should be strong enough to garner interviews to at least a few of the MSTPs I've applied to, and so applying to more schools that I have no interest in attending is not something I plan on doing at this point. In the worst case scenario that I don't get any acceptances this year, I would much rather take a year off to get a 35+ MCAT score (given that my first MCAT was a self-study and taken after my sophomore year of undergrad while I was totally stressed by working full-time) and to strengthen my application with more research and clinical experience, then re-apply to a competitive program, than to matriculate in 2009 into a weaker program in an iffy region of the country with research opportunities that may or may not be in my field of interest.