The only thing I can think of offhand is that if your clutch spring isn't centered properly, the front end of the pushrod won't seat properly. The clutch parts align so that there's a hole where the pushrod end goes in. If the clutch spring is out of alignment, the pushrod won't go in all the way and you might not notice it because it looks like it's in all the way. If the pushrod isn't all the way seated in the clutchpack, then it will protrude out the rear end of the transmission more than it should. Having said that, if it's not seated all the way, I'm not sure you'd be able to get the transmission on at all....
Anyway, it's something to look at. Read through this thread, I describe the problem with the pushrod not going into the hole all the way in detail and give you some measurements to work with.
Hang in there...
MH