Cuttoffs aren't necessarily set in stone--I had two interviews at programs where I didn't meet their cutoff score, and I didn't have the research background you do, though I don't know if increasing interest in the field is changing competitiveness (I think our board scores are still the same--ie, fairly low). Your research background will likely help you a lot, as well as your step 2. 60 programs may be overkill, but I'm also being told by current M4's now that the goal is to interview/rank about 16 programs or so, whereas when I applied the goal was about 8 (to have a 95% chance of matching per the Charting Outcomes in the Match data).
I'm not sure how accurate that 16 number is (I never looked at the most recent data), but applying to programs is fairly cheap--it's easy to cancel interviews if you get too many.
Applying to 40 pre-lims does seem like a lot though... I just applied to the 20 or so programs within Chicago, and only my own academic program and community programs (I didn't see a reason to do an academic pre-lim unless it was at my advanced program or current school--they're typically harder hours and you see more zebras, whereas as a PM&R resident you really just want to get comfortable with bread-and-butter medicine). I thought it'd be a waste of money to travel around the country for pre-lims, so unless an interview was coordinated with the advanced program I applied do, I didn't bother applying to pre-lims in different geographical areas, aside from a few TY's within a 5-8hr drive or so.
Don't forget to apply to TY programs--they're much more flexible with electives. Just try to apply to programs where you'll actually learn something--most of the cush programs out there are not going to help you get a strong background in medicine, but typically the less competitive TY programs that PM&R residents are more competitive for have a good combination of electives, good medicine rotations, and a better schedule than many pre-lim IM programs.
