Well, partial success at any rate.
When we left off a couple weeks ago I had opened up the gearbox to replace the kickstart pawl and couldn't get it back together.
The secondary shaft had pulled forward from the bushing it rides in at the back of the box and no amount of finagling would get it back in.
This morning I pulled the outer primary cover, generator and clutch basket, which allowed the primary shaft to slide back and forth.
That allowed me to move the secondary shaft around enough to slide it back into the bushing. I have also decided that part of the problem was that the slot at the bottom of the shifter bell crank was not properly engaging the pins on the shift fork. This kept the secondary shaft from moving up and down enough to get the end of the shaft into the bushing.
So, to wrap up, I was able to get everything in and lined up and slide the shaft back in place and put the inner cover back on.
So tomorrow's project is to reinstall the rest of the shifter assembly and outer transmission cover, pull the inner primary cover, replace the countershaft sprocket, install the shift improvement bushing kit and heavy duty clutch springs and reassemble the primary.
Not too much.
BTW, Snidel says that before you remove the inner primary case you have to remove the electric start sprague clutch assembly. how are you supposed to do that? 2 of the 5 screws that hold the cover on the assembly are not accessible if the inner primary case is attached to the crank case. I was able to pull the generator and primary chain sprocket without pulling the sprague assembly and it seems like I can pull the primary cover with the sprague in place.