Your boss sounds like an unbelievable prick. And a dimension no one has mentioned is that he knew you were applying to med school and could conceivably quit at any time, yet he gave you no forewarning that he would hardball you. You need to stand up for yourself.
Assuming you didn't lie on your apps in any way that he could expose, I can 't imagine he could do anything to get your admission rescinded. It is actually kind of a good thing that his recommendation letter came later. He signed that letter and now, presumably not much later, he's changed his mind and will sign that? Sketchy.
Step 1: Begin to document everything, as someone said. Send him email and see if you can get him to put any of this in writing. Get your own written documentation. For example, you might send an email to a friend or someone saying what this guy is doing and that you believe and have had every indication that you've performed well, etc.
Step 2: Talk to him. See if you can talk him out of it. Try to find out why he's doing this. Also, in the process, try to find out (if possible to do tactfully) what exactly he is planning to say/do in the "revised" letters.
Step 3: Assuming that doesn't work, I'm not sure. But again, I don't think you have to worry too much. I would just go ahead and quit. Maybe offer to give a couple extra weeks as a compromise if that works for you. If you can find a way to consult with a lawyer without paying a huge amount, you might want to do that.
By the way, are you waiting to hear from any schools that are important to you? It's much less likely that a school is going to rescind an acceptance on this basis than that they would change their mind about accepting you.