Steve What bell housing are you using and was it centered on the crank? If you smooth the end of the trans with a belt sander, (round the nose) it should side in with a touch of grease. You may have the wrong pilot bearing if you are using a GM input shaft on the trans. Use 2 steel rods to hold the trans up and inline. It should slide in. If you need to wrench in the trans the last 1/2" the problem is the pilot bushing, and you will push it until it bottoms out in the crank, It may go in, it may not, You may have to get a small brake hone and clean it up on the inside. YOU WILL break the ears off the trans by wrenching it on with the 7/16 bolts.
If you have alot of pressure on the pilot bearing you may wear out the crankshaft thrust bearing surface and the motor is short lived. This is why some guys do dry runs with the trans outside of the car before installing motor or trans. Rick Lake