The motors are identical, heads and blocks. All parts can be swapped. The later E36 got a different chain tensioner setup - it has a deflection rail instead of an idler gear. AFAIK there are also three accessory belt systems too - v-belt, belt & serpentine, then full serpentine. E30 has the two-piece front sump pan. E36 has the one-piece rear sump pan.
There are a few electrical differences too - EWS DMEs - the DISA manifold (dual-resonance intake) - knock sensors. The cyl head temp sensors are combined on the E36 as well. Later E36 motors have lighter rods and thinner valve stems.
I typically pull the motor and transmission as one unit. Those reverse torx bolts are hard to undo in the car. It's also possible to drop the subframe instead of lifting the motor.
As for the bottom end, I'd use the same values as the M50 if they're listed. I did a quick Googling and
found this cool site though. BMW's TIS workshop manuals online.