The bell housing and starter tip may still need a little clearancing for the pressure plate.
No, that's not the reason. Probably the reason it won't go in easily is because of the clutch slave/throw out bearing. Put a c-clamp on the clutch release lever to hold it all the way UP and it will slide in easily.
I would recommend installing the engine to trans bolts and starter. Then rotate it by hand a few times. If you don't feel anything, then bump the starter a couple times. Then pull it apart and see if there is any clearancing necessary.
thats why you supposed to turn by hand.. i watched guy pull engine 3x and pan.. cause he screwed up main shaft length then thinking bottom end locked.. back in 96...
no no listen to me on main shaft length.. libby should know that one.. when people put diesel bell housings on the non diesel tranny the main shaft has to be shortened... your issue is 02a flywheel crap.. he figured out his mistake when he learned loosing up all bolts to tranny 1/2 turn allowed stuff to turn again... but libby said turn by hand as you tighten it up.. so thats why.. he learned long ago on that silly stuff.. the engine really should roll over nice by hand.. if you need a cheater pipe.. id rethink your work... cam cap, main cap is on backwards.. something.. any engine ive rebuilt i can turn by alt with wrench/socket where v belt no slip...
no no as in no do not... ignore mainshaft... unless you built custom tranny too..