Wow It's been a long time since I've had one of these transmissions open. It sounds like you didn't get the reverse shift fork lined up properly when you dropped the shafts back in. If everything else works fine then it's got to be inside. Unfortunately you're going to have to take it back off and open it up to fix it. Look at the linkage to the reverse fork and make sure it is moving the reverse gear up and down properly.

Sorry you didn't get it on the first try but I'm glad it helped. When you get it back open if you still aren't sure post some pictures and I'll try to help as much as I can. I'm subscribed to this thread so I get e-mails when someone posts. So I should be able to reply within 24h. Good luck!