Welcome to the site.
If you did a little bit a research you would have answered all of your questions yourself. In my M52 swap thread I ran into every problem you did. Turns out they weren't problems at all.
The shifter sits forward a little bit because you have to bend the arm downward with a vice, making it more of a U until you get the desired adjustment. It's cake.
I would go with the matching engine mounts from which the motor came from. For example, my M52 came from a 328i, so I purchased 328i engine mounts (not 328is, 328ic, not 318, not M3). Any mount will work just the same, but I went with the 328i mount to keep things as simple as possible (and budget).
The transmission mount holes won't line up where the old "o" shape hole is, you have to use the oval hole, which shouldn't be a problem.
Do some research, there are plenty of M52 swap threads on here to go off of. Trust me