For what it is worth,
1. Research interest matters little to the mentors with which you work with. I don't think this can be overemphasized.
2. I am can bank most of my money on a MSTP program having a usually fabulous selection of thesis labs to choose from and great mentors. (The school got the MSTP grant for a reason) Now, this is not going to go across the board and put great mentors doing what you want to do at all (or even most) schools. But odds are, there are still going to be good faculty in the same or a similar department. Hence...
3. The difference between in working in an NMR v. crystallography lab, or bacteriology v. virology, or micro dept. v. immuno dept. is actually pretty minimal in the long scheme of your training. I don't know the specificity of what you define your current "field" as. However, I am betting you can find a plethora of future mentors if you branch out a bit. How drastic that is, that depends on your situation.
4. The point of going through all these different steps in training has a variety of reasons. One of which is that it forces you to learn new things, meet new people, and take different steps. Because, part of the award is for you to learn new stuff and do different things, not just doing some solid techniques that you have done a ton in the past. The NIH and other fellowship funding agencies view stepping outside of your previous comfort zone as positive. Just something that I keep in mind when I get in similar sorts of situations and faced with doing something that I have no experience doing.
5. Three years of research is not enough to make a career decision on, especially when you have just scratched the surface in undergrad. Look at the open road, and not the light at the end of the tunnel. Most scientists will switch directions more than once in their life.
6. Reapplying is hard and risky. Because you haven't been really working on it during the previous app cycle, you won't be able to make significant improvements in your app by June or August. You will be asked about why you didn't take one of two acceptances. Don't apply to schools next time that you wouldn't be happy at for MD-only or don't have research options for MD/PhD if you try a mulligan. Don't get stuck on single mentors, focus on good departments and collections of mentors.
Just some food for thought. Good luck!