Is there some reason you want to do your MD and PhD at separate institutions? Is it based on where you were accepted and you aren't happy with research potential at that school or are you not happy with the med school at the PhD granting institution? Out of curiousity, are you wanting to move cities for this or is it next door? When you're picking an MSTP, you're usually picking the whole package - MD and PhD. If you're not happy with the whole package, you might as well just do the degrees separately (maybe take a LOA from med school to preserve the MSTP structure) and save everyone the headache (especially if you're considering covering the MD costs yourself).
Remember that your post-doc will ultimately be the most important lab experience for your future career as far as obtaining faculty positions, finding the direction your own research is going to take, etc. That might be the best time career-wise to work with that fabulous PI you want to switch institutions for.