Does the 'new' transmission come with the bell housing intact?
For example, if the transmission were coming from a diesel and going to
a gas engine, the bell housing would have to be changed.

I hope you are  not changing the bell housing but if you are, careful
and tedious attention to detail of fine print somewhere in the shop docs.

IF the bell housing is replaced, there is a procedure to set shims for
the nose piece from the transmission and bell housing. if this is not
done properly, in some thousands of miles, the extra play of the nose
piece will eat out a conical section of the inside front of the
transmission case and it makes a terrible swift sound on starting forward.

trust me. been there. done that. ain't fun. and the solution to
prevention is definitely a trivia question to separate the truly
experienced master mechanics and i don't fit in that category but i did
learn that bit of trivia (with an 85 745).