I read somewhere in here that it is a BIG no no to try and mate the transmission to the bell housing by putting in a few bolts and tightening them up.. but how close does it have to be for it to be ok?

Someone give me some peace if mind.. the damn drive shaft would go through the clutch but have trouble getting in the pilot bearing. Took it all apart, re centered the clutch and gave it another shot and the transmission came pretty close to flush with the bell housing so I felt confident that at least some of the drive shaft was in the pilot bearing.

Tossed a couple bolts in and it went together, didn't hear any grinding, breaking or anything. Am I good?

This is how close it was before putting the bolts in.

 

that's close enough, you can do the rest with the bolts. The issue occurs when it's not on the dowels, the nose of the shaft is not centered in the pilot and/or the clutch splines are not aligned properly. Then you will break the case or strip the BH threads.

 

Ok great! It was weird, when i initially did the swap it popped right in by shaking it a bit. I guess that clutch disc needs to be near perfectly centered. Ill keep that in mind for next time!