Depends on the mileage of your car and what you'd like to do:
I believe the 335 (assuming that's what you are doing) has aluminum use-once bolts (they stretch). If so they should be replaced with new aluminum bolts or steel. Make sure your output shaft seal on the back of the motor isn't leaking, once the flywheel comes off. If I was dropping the trans, I'd rebuild the shifter assembly parts as it is cheap and right there. I would also do a short shifter, probably swapping in a different BMW shifter vs going to aftermarket, but either way works. A Google search provides options - even BMW has gotten into the short shifter game as they sell a "kit", but it can be done cheaper. Check the output shaft seal on the transmission (they are typically fine in my experience). If you've got good miles on the car, I'd consider replacing wearables in the driveline - flex disc right behind the trans (it's rubber and gets disconnected) and the complete center bearing support (one can buy the bearing alone or the complete assembly - Rein complete assembly is like $65, which is what I'd do). I'd swap trans fluid, especially with the short shift setup - my fluid of preference for the short shift setup is Royal Purple Synchromax. Others may suggest Redline.
Aside from the aluminum stretch bolts, you don't have to do any of the above. But that said, those are the items I'd be looking to do if I was doing having the trans out of the car. Good luck!
Filippo