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.

Can also back the trans all the way out of the clutch disc. Put the trans in 4th gear and put the drive shaft in the tail and rotate it 180° then try her again, with the trans in neutral.