I've asked this same questions to friends who have already left for grad school/med school/both. I also asked a lot of graduates when they came down to my university for a poster session/ meet and greet. A couple of things pop up:
1) ask the current students, especially the ones that are almost done, about resources for graduate students and MD-PhD students who are struggling. Who do you turn to if your advisor leaves, you feel like quitting, your lab environment turns out not to be a good fit, you are depressed because many of your friends went on to clinicals, you feel burnt out on science etc. Essentially, who do you turn to when things are not looking up and how effective are they at working stuff out or at least helping you cope.
2) ask about the specifics of entering back into the clinic. Do they give you some time to brush up? Do they have a structured way to keep up with your clinical skills during grad school? Does it actually help students and work as intended (another great question for PhD M3s/4s)? Does the school give you the option of coming in with a new batch of M3s on your first rotation or are you forced to jump in the middle of an MD only group with weeks/months more experience from the get-go if the schedule works out that way?