3 speed or 4 speed? Sometimes it helps to turn the output shaft a little bit to line it up with the disc. Some shaking may make the difference as well. Usually the rear of the transmission is hanging to far down. This causes the pilot shaft to hit the pilot bearing/bushing. Try lifting the tail of the transmission and pushing it in.

Another trick is to use 1/2 inch 13 thread rod on the top 2 holes. You can then suck the transmission into place with some 1/2 inch 13 nuts.