Blue Ox,
When I disassembled the unit, I carefully measured and marked the relationship between the nut and the pinion shaft so as to reposition the pinion relative to the ring gear as closely as possible upon reassembly. I did not, however, pay any attention to the relationship between the pinion shaft and the yoke itself, resulting in having no idea if the yoke was times with the pinion shaft in its original position. In light of the fact that I was replacing the bearings, I opted to replace the crush collar with a replacement obtained from RingandPinion.com (a great resource I might add).
Upon reassembly, I carefully seated the new bearing cups (races), oiled the bearings, installed the pinion seal, then the pinion shaft with the replacement bearings installed, followed by the yoke and the nut. The nut was tightened to nearly the same position relative to the pinion shaft as it was originally at which point the preload torque was checked and the nut gradually tightened with preload checked at each interval until the desired preload on the pinion shaft was achieved. At this point the ring gear carrier/differential was reinstalled followed by the axles, cover, oil, etc.
Hope this answers your questions. Thanks for your interest and feedback.