well, i applied to med school ages ago but from my experience i can tell you that a lot of it makes no logical sense and its not a foolproof system. a few great people get rejected while a few subpar people get accepted. in the end, most people who are good candidates get in and it all works out.
i remember i had a 4.0 and a 42 MCAT (back when the top end was 45, i have no clue what it is now) and at many of the schools i interviewed at many of the interviewers seemed like they were almost begging me to come to their school but in the end i was rejected by them. one top tier school, i even had a glowly letter of recommendation from one of their own department chairs who i did research with during a summer in college. and yup, they were one of the schools that rejected me. to this day i have no clue why and honestly, in retrospect it didnt matter at all. im in a great residency now and i had a wonderful time at the med school i went to.
so i know this stuff is troubling for you guys now (i know i was stressed out), but i just wanted to let you guys know that it all works out in the end for the vast majority of you and if you dont happen to go to your top choice med school, it's not the end of the world (like i thought) and you can still have a great time in med school, find a awesome residency and become an amazing doctor.
good luck to you.