It sounds like you have a fabulous pdoc. The bad lipid results may be from the antipsychotics you've been on and it's good to see that he did an A1c level. Fasting glucoses are good, but can be misleading in someone whose sugars they're monitoring.
It sounds like the Master's degree option may not be a bad one if you don't mind adding another year. Would you be guaranteed a spot in rotations if you were to take another year of didactic instead of clinical studies? It sounds like you've at least got some options and you're young, so you do have plenty of time to work on it.
Something else to keep in mind, just as a back up....if for some reason things don't go well in rotations, you could easily get into a physician assistant program, which I believe is a bit less rigorous in its clinical rotation work (ie: no sleepless nights). I may be wrong, but that was my impression when I was looking at PA programs. I'm certainly not saying to give up on the MD, but don't lose hope if things don't work out.
Oh, and yes, it makes sense to not feed into the OCD with an overly detailed field like pathology. I was just thinking it could be a good option to accommodate that if you were struggling with the frenetic pace of office-based managed care. Internal medicine sounds much more agreeable than emergency medicine or general practice.