Cal you are correct... I am getting befuddled by piling up the issues and looking for an overall solution.
I was going to post a few more comments and photos after my last post but I got distracted by going to the pub.. I tend to find this happens a lot?
I can address a few of your questions quite quickly...
"It's hard to see from the pictures, but is the rear wheel assembled with the correct spacers? Does the rear wheel (rim) spin freely and without obstruction on the axle?"
This was my first assumption and I have checked and checked again and I can only conclude that everything along the rear axle is correct.. I will post some pics as a fresh set of eyes may pick up something I have missed. The rear wheel spins beautifully on the rear axle and there is no obstruction.
"For the front end, first thing I'd do is to release the tension on the triple trees and allow the forks to be adjusted. But, is the steering stem bent is my concern? This would show by rotating lock-to-lock and feeling for rough spots in the steering bearings, and leveling the underside of the lower and comparing it to the upper clamp."
I did release the tension in the front forks and this led to my next discovery... bent front fork tubes. (see Pictures below). No idea how i missed this? It's subtle... but they are bent without a doubt. Hopefully I can get these straightened? A bent steering stem or frame is still a real worry though.. particularly if I know I have bent forks, misaligned sprockets and a ding in the alternator engine case.
There is definitely no rough spots on the steering head bearings. I replaced the bearings with new All-Balls tapered bearings and they run real smooth. I double checked them and they are installed ok.
When I installed the tyres I tested the wheels for 'trueness' on a jig and I was happy at the time that they were good. I will double check again.
As suggested I will go back and check the sprocket alignments with the straight edge and follow your 3 steps below..
Your suggestion of setting up the string box is interesting and a method I've not heard of before... I'll give it a go.