Hi all,
My first post on these forums. Anyway, I've done exactly what you're proposing. Quite a few people do it at the Vanderbilt MSTP (almost 30-40%) in the last year or two. I personally feel that it is an excellent path choice, because you get to go thru the clinically relevant part of your pre-clinical training (Path, Pharm, Pathphys/LabDx, PhysDx) right before you actually get into third year. And I feel this is quite important, because after 3-4 years of science your path and pharm is very rusty.
Furthermore, it takes (from my experience) about 6-9months to retrain yourself to think like a medical student again (regurgitate facts, generate differential Dx) compared to my preferred scientist thinking method (analyze, criticize, re-evaluate). One does not want to look like an idiot during his important 3rd yr rotations.
Boards-wise, it may be a little more difficult, but only a little, because it does not take too much time to brush up on first-year stuff, which is not that board-relevant anyway. Significantly more weight is placed on 2nd yr material. Also, after years of reading and keeping average residents hours in the lab (60-100), getting into 2nd yr instead of a third will seem like a nice break with free time and everything, to leisurely reenter the MD field. All that class and Boards stuff is much less stressful after you've gone through the stress of paper reviews/rewrites and thesis writing/defense.
Just my 2c.
Aleks Stanic, Ph.D.
Vanderbilt MSTP