Your MSPE (known as the dean's letter) usually has a histogram of how you did compare to your classmates in every class during the first two years, whether it's pass/fail, or letter grades.
Unless you are gunning for very competitive specialties, how you do during the first two years of medical schools, in the grand scheme of things, are not very impactful or significant. However, if you have any red flags (held back a year, academic/honor code/professional violation, etc), it can hurt you.
How you do during your clinical years are also important, and probably more so than the first two academic year. I also look at Step 1 and Step 2. Together with your interview scores, the composite of all the above will be quantify and you will be ranked based on the total score. Of course, the PD (and the residency selection committee) can go over the list, make adjustments (move people up the list, move people down the list, drop people from the list) before submitting the finalized rank list to NRMP (or AOA NMS)
A low step 1 score raises some concern, and I will focus on the LORs, clinical evaluations (and histogram), and Step 2 scores to make sure that Step 1 score was a fluke. It doesn't cancel out Step 1 performance (since it is still factored into our ranking), but when we review the list, we might be more incline to move someone up the list (who was rank lower than we like based on total score, including Step 1) if we overall like that candidate and the only reason he/she is ranked lower on the list is the Step 1 score.