If you don't have the disc properly aligned with the crankshaft, the transmission shaft will engage the disc but the pilot surface will bump into the pilot bushing or the crankshaft. It sounds like that situation is what you have. If you don't have the proper alignment tool to position everything properly, you can slide the clutch shaft into the clutch assembly as far as it will go, then loosen the pressure plate so the disc is loose enough to move around, then push, shove, and wiggle the transmission until the clutch shaft slides into the pilot bushing. Secure the transmission, then tighten the pressure plate bolts- evenly, each one on the diameter from the previous one. If the transmission case doesn't slide fully up the the bell housing, don't tighten the case bolts hoping to pull it into place- you are likely to break something.
You should be able to rent a clutch alignment tool from a local auto supply. Its worth the couple of dollars.
Also, it does help to put the transmission in the direct gear for all this, but a lower one won't hurt anything- its just harder to turn the tail shaft if you put the transmission in a reduction gear.
Harvester
