Hey Mike, A few thoughts,
If you replaced your circlips on the trans is it possible that a gear may have gotten flipped around during assembly ?
Is the dowel pin on your shift drum still there? Just a thought, if its missing you might not have the drum matched up right on either side of the case.
You are sure all of your forks are sitting correctly in their grooves and nothing is jumping loose on you?
What year is your crankcase, what year is the trans from?