need help

okay so my buddy scored a 22r motor with 2500 miles on it out of a 2 wheel drive truck for 550 buxs got it home changed the oil pan and pick up tube mounted the flywheel and poilt bearing installed the new clutch pressure plate and threw out bearing. got the motor in the truck and now we can't get the trans to bolt up all the holes line up but there is a half inch gap on the drive side between the motor and trans put it in an 86 toyota 4x4 any ideas?

a burr on the clutch disk
clutch disk not aligned properly
make sure the clutch disk slides onto the transmission shaft (you'll have to take it off of the flywheel to check)

Yeah, do that. If everything still seems fine, you may have to pull the engine on with the bolts if you can get enough thread to safely do it. That's what I did. By the way, did you put any grease in the clutch where it slides onto the tranny shaft?
If there are two of you, one of you should work the motor on while the other one turns the transmission pinion from the rear of the tranny. You will either have to raise the rear and turn the wheels or disconnect the driveshaft. Make sure the tranny is in neutral.