360 instal, going on 3 days, need help

Every time I do a clutch on any car,I slide pilot bushing on first to check fit and the I slid the clutch disc to check if it slides easy.I have had more than one clutch disc with a burr in one of the splines that was easy repaired with a file or simple cleaned up after sliding the disc on and off.
Many ,many years ago,I tried and tried to get a tranny to go in till I pulled the clutch disc to find a little burr on a spline.

Ever since that one car it has been Common practice for me to check the disc and pilot bushing/bearing
By force the tranny on,I hope you at worst only bent the clutch disc.But like 67Dart273
said maybe your disc is on backwards and hitting your flywheel bolts.
Now that the motors in,pull the transmission...
The number one rule installing standards is alignment.
1. Clutch alignment
2.Tranny to engine alignment going in top to bottom and side to side and it should go right in.Try getting it aligned by jacking up or down the motor till it is aligned to your transmission on your jack.
Good Luck and keep us posted.
TXDart.
It is a lot easier for me to do them on a lift with a tranny jack that I can set to any angle to get my alignment perfect.I use to do it with floor jacks and even putting on my belly and man handling it in.