Congratulations on wrapping up with the toughest part of the program!
That said, you will probably find the first few months back in clinics challenging (as does almost everyone) - and there are two things that make me a bit concerned in your situation:
1) You're coming back off-cycle and will be graded against classmates who've been at it for 6 months and for whom expectations are higher. It would probably help to mention to your teams (but not dwell on this point) that this is your first clerkship back from the PhD, etc. etc. just so they adjust their expectations accordingly. Unfortunately, residency matches for almost all specialties are getting more competitive even for MD-PhDs, so it really helps to do well in 3rd year.
2) You're starting in medicine, which at many programs is the toughest clerkship. At the start, worry less about the book knowledge (which you will pick up), but it's more being able to function on the floors, knowing the workflow, knowing what to look for on prerounds, knowing how to present patients with a plan, etc. etc. that might be difficult to begin with.
Alas, the book knowledge catches up with you at the end for the SHELF exam which I thought was the hardest of all the core clerkships - here don't read textbooks but read review books and question books (see other SDN threads for which ones to use. Textbooks are basically useless for clerkships unless as reference for something you totally don't know)
My advice with all this - after your defense, make book-studying priority #2 until the clerkship. Make priority #1 having some way of getting to know how the floors work. Ask your IM clerkship director if you can hang out with a medicine floor team for a few weeks before the holidays in some semi-structured but non-graded way (our MD-PhD program actually offers this routinely to all returning students and it's been a huge help). If this is possible, pretend this is your clerkship, take it seriously, and go all out to get up the learning curve. Also, talk to other students who've gone ahead of you to see what they did to smooth the transition.
If this is not possible - see if one of your MD-PhD mentors is on service at a time you can shadow. Especially if they're responsible for a service, get to know the residents and see if they can let you function as a floor med student.
Option 3 - shadow someone in outpatient. Helps with exam/assessment + plan skills, but a bit less useful for floors.
Good luck and PM me if you have any questions.