At first I was thinking that maybe the PI is jealous of med students or something, because some PhD's are that way. But that is not the case as their were med students as well.
Most likely you did not perform too well. The PI is obviously qualified and has a number of medical school students and PhD's working under him, so I suspect he knows what good performance is.
If I were you, I would not get any letter from the lab. Why do you think he would write badly about you? Is he jealous? Vindictive? Or just being honest? If he is honest, what if the other person is honest as well? Sometimes you are unlucky and get a really strict person. That seemed to happen to you.
MCAT, grades, and EC's can be overcome, but if medical schools even suspect you are a liar, or have personality difficulties with others--unfortunately, that is automatically rejection.
So you have to be very careful. You have a poor chance at the ones you already applied to because they suspect you lied. If you mess up this third round, your chances are really limited.
You have very good stats, so, you can easily get in without a letter from research. Just focus on other stuff besides research because, obviously, if you emphasize research it would look suspicious. Good luck!