dixie wrecked

iTrader: (6)

Hello all.. Recently my 334 became a 334c.u. v6, so this weekend the motor got yanked out. New ones in, yada yada. New clutch, pressure plate, throwout bearing, flywheel was excellent so I just hit it with some 1000 grit to remove the glaze. Anyway, the motor I got was from an automatic vehicle, so no pilot bushing. So, I installed one. Used a rubber mallat, large socket wrapped in a towel and popped it in. Almost in, the socket punched through the towel and beat the surface of the bushing some..however, the clutch alignment tool still went in smooth, and didn't scratch up.

Putting the trans in (which really sucks when you let someone borrow 2 of your 4 jackstands), it wouldn't quite seat fully. Had a helper engage and disengage the clutch, no change. Was maybe 1/8" off. Frustrated (and needing to get to work tomorrow..) I just used the bolts to pull em in. They went fully in and sucked the trans in with very little resistance. I didn't have to put any muacle into it at all, didn't force it to turn. None, Nada.
That being said, what are the chances that that will damage something?
Idiot question of the day, I'm sure. This is the first manual trans I've ever touched, so not 100% on everything.

I did use the alignment tool as well.
Still putting her back together now..