I painted the cases this morning, and found a spare couple hours this evening to put the bottom end together. However, I committed a serious rookie move, which will necessitate I re-split the cases tomorrow. I won't admit to what I did unless someone can guess it...
Anyway, before the last tear down, the shift fork shaft had pushed itself outward towards the clutch side, bending the retainer out a bit that holds it in place. The shaft rests in a hole, and I think what was happening was that air was getting trapped behind it, then expanding when the engine heated up, pushing the shaft out until the pressure was released. I think I mentioned this back in this thread somewhere. Anyway, I decided to fix this problem by drilling a relief passage in the end of the shaft.
First I chucked the shaft up in the lathe and used an end mill to hollow the end of the shaft:
Then I cross-drilled a relief that would vent into the inside of the case:
After I fix my brain fart from today, I just need to track down a base gasket and I'm ready to reassemble... finally.