It's been a while, but progress has been happening.
Rebuilt the u-joints, and that is not a fist-fight I recommend having but it's done now.
When re-installing the rear swingarm, I heartily recommend leaving the final drive off so it's lighter, and install it afterwards. And then I learned that the swingarm doesn't like to go straight in, but instead tip it up-and-in at a strong angle such that the brake-side swingarm pivot bearing goes into the pivot-pin pocket on that side of the frame...in this way, using the depth of the pocket makes it such that the whole swingarm just pivots up and into the frame without any fuss at all. Have the pivot pins handy so you can put them in without dropping the swingarm on the floor. (thank heavens for this forum and "search", btw)
We're now entering the "finished carpentry" stage, which in my view always takes the longest if you're going to do it properly.
First, he's starting to look like a motorcycle again...

The tedious business of what has to be installed before what is now in play. Starting with the rearsets and shift lever. When I got the bike, the p.o. had bent the left hand rearset way back - I had thought it was to clear the Dunstall silencers with no h-pipe...that put the flare of the muffler really far forward. Thanks to Charlie I have an h-pipe now, and the silencers are now going to sit further back - once I repack the silencers and make brackets noting that the mufflers were unsupported previously and just hung cantilever off the back of the down-pipes. (...sigh..)
However, I still had to do a lot of messing around with shims and spacers to get a rearset+shift position that works. What's shown is pretty workable with some but not terrible clash; I don't like all the spacers and on downshift to 1st the shifter just skims the rearset and the pipe and will leave wear marks eventually.
Does this look right to you all, and any tips on getting this area to work nicely? The link from the shift pedal-rod bell-crank to the gearbox is shortened as far as it will go - possibly if I pop the gearbox side lever off and hop one spline, I can get more adjustment back and then 1st->5th will all happen *above* the rearset? Since it was messed up when I got it, I don't know where this lever is supposed to sit naturally and whether the shifting happens on both sides of the rearset or only one side.
I'll ride this as-is, but if I can clean it up, great. I also see that the cap-screws are too short now, and nylocs are too tall - so again, a wierd fastener situation here that I have to rectify.

Post-post edit: I popped the arm off the gearbox and rotated it 1 tooth - now 1st->5th is entirely above the footpeg, and I was able to pull 1 turn out of the pedal->gearbox link as well. I tried taking one set of the spacers out and the shift lever would still hit the footpeg, so with all the spacers in, the shift lever has full travel and hits nothing. Still not sure this is right, but happier with it.