I'm finally getting around to putting the bike back together. Thanks goes out to Sean with help on swingarm surgery.
Rebuilt the output shaft last night. The OE one felt a little rough once I put the new yoke on. Not sure if I tightened up the pinion nut a bit too much or what. I figured a I should not install something that I did not feel good about. I decided to dissect the donor output shaft to see how this thing works. I was expecting it to be a major PIA but really, was not too bad at all.
I pressed the pinion out of the donor carrier, removed the crush collar, then did the same with the OE unit. I put the OE pinion in the donor carrier, measured the crush collars and used the longer of the two and reassembled. Put it back together so now I have OE pinion in the donor carrier with the yoke assembly. I was thinking about doing this from the beginning because I was unsure of the condition of my output shaft seal and the carrier looked like it had been thru hell. Now, it looks like new. I used a thread file on the pinon threads as the end of the threads were distorted from being staked and filled with thread lock. Cleaned it all up and slowly torqued while tigtening the nut. I was able to hit the torque spec and still rotate the bearings. Everything felt right, the bearings turn with little rotating torque and I could not detect any play.
I staked the nut, installed a new spicer u-joint, installed the second half of the yoke, then put the output shaft back into the bike and shimmed it up.
Hoping to get the rest of the bike back together soon so I can test it out!