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

Sounds like its either hung on the bearing retainer or the crank pilot bushing. Is your engine a factory manual trans? What all are we working with here, engine, trans car wise? We need more info

If its not a factory manual trans engine you might need to modify (i.e. shorten) the trans input shaft end and use a pilot bearing and adapter that goes in the torque converter hub bore on the crank.