Transmission stuck 1/4 - 1/2 out of bellhousing when reinstalling

I would take the 4 mount bolts out of the trans ( with the engine supported ) then see if you can rotate the trans to see if it is locked tight to the bell housing.

You should be able to rotate the trans if all parts are the correct ones.
I tried to take it out of gear and rotate it but it doesn’t any more now that it’s further in I wonder if the pilot bearing is the wrong type then