There is a thrust washer between the case and the end of the gear cluster, to keep the gear cluster from shifting back and forth and it will bang into the case if it is worn out or missing. Other than that, I would have to look at the trans to see what is doing it. I am in Des Moines, IA, a little far to go.
Is this trans and motor combination original? I know if you try to match up a different trans and motor combination, you have to check alignment of the bell housing, or it will give you all kinds of trans issues, including popping out of gear. Tolerances are supposed to be pretty tight on the bell housing alignnment.