Got the case halves reassembled. Put the tranny in upside down in the bottom of the case and had a friend help guide everything in while I set it down.
I almost screwed up the kickstart mechanism until I decided to look at it carefully. I had the 'nub' on the large ring sticking up instead of down in the keeper. That left the mechanism engaged all the time and whenever you turned the transmission you get the constant clicking sound. Tried the other position 180 degrees away and hey, that makes more sense. In the service manual the only picture of the kickstart shaft shows the gear engaged - that is pretty confusing.
Good thing lots of people on here take pics of their rebuild, I almost left off the bearing retainer ring for the shift drum until I found the part and went back through a bunch of builds to figure out where it went. The factory service manual is almost useless for most of this with the number of errors it has in it. After putting all the shifting mechanisms back together I put the shift lever on and ran through the gears. The damn thing actually works!
I'm going to go with a dynoman 592 piston set, but that is a lot of dough and I don't see getting this thing done for riding this summer so I'll push that back, seal up the motor and get back to working on the frame and suspension.