I did use a clutch alignment tool. It slips in and out with no problem. I've tried installing the motor with the car in gear and in neutral. The through out bearing moves fine. The pressure plate is not far enough back to touch the bearing so it must be the pressure plate that is catching.

I'm trying to avoid pulling the trans because I would then have to pull the exhaust, driveshaft, shifter linkage, etc. That's my last resort if I can't get the engine on with the trans in the car.