I found the problem with 3rd gear. (old gear from the barn’s junk pile for comparison) How the heck does this happen? The spline on 3rd separated smashing the sychro ring and making nearly impossible to shift into gear without a lot of finesse and sometimes a crunch. It looks as if it was never apart since it was built. The only explanation for why 3rd was whining like a banshee, is that the input shaft bearing was worn out.
The engine is back from the machine shop, so I can start on that after the gearbox and OD are re-united later today.