Full disclosure: I am also on the MSTP WL at Stanford. Because of that. I can’t rly weigh in on this in good conscience, but I will say that research wise the decision looks like it comes down to Stanford or Michigan for you. Reiterating what the other person said, the weak dept and lack of PI depth to work with at Vandy is concerning and would, for me, be a dealbreaker. PhD is half of the MD/PhD experience and you should go somewhere where you are confident you will have breadth and depth of resources for your interests and be well supported.
I’d say definitely go to second looks and rly try to get a feel for the programs (culture wise and also talk to more PIs! Maybe Vandy can still surprise you) and see what is the place where you feel you will be happier, more productive, because that will also determine your success. In terms of impressivenss of match list I agree it’s Stanford > Michigan > Vandy
Congratulations!