So...had the pinion shaft in and bearing preload set. Had the countershaft in and bearings set. Was installing the input shaft, had it all together, torqued the stake nut, turned it to get the slot up, took a punch and went to set the nut, smacked the punch, heard a pop and the nut fell into the bottom of the transmission. Got it all back apart and it turns out the shaft already had a old fracture right where the threads ended.

So now waiting on the shaft, already have the differential in and reshimmed for endplay and pinion play, installing axles and bull gears this afternoon.