I mark the nut and shaft with a punch, back it off (I use a rust dissolving acidic penetrating oil), clean up the the threads, oil and torque the nut until the marks line up (remember the torque reading). Reinstall the new yoke with the same torque, usually around 150 ft lbs. I think the book says above 160 ft lbs-260 ft lbs. I have a three foot long 3/4" drive torque wrench, a hundred and sixty pounds of torque needs a big torque wrench or a lot of butt.
If you have the carrier out you can double check your pinion bearing pre load (usually loose with older bearings), usually measured in inch pounds. Check the bearing for smoothness and low noise, feel for hitches and other signs the bearing may be worn out of round or extremely loose.
Without removing the carrier, I turn the wheels to the front, remove the calipers and disc, turn the yoke with my hand. Put a torque wrench on the yoke nut and see how much effort is required to turn the yoke. I can often turn it with two fingers and a thumb, I usually do it mostly by feel.
I try to reinstall the yoke without things tightening up too much. They shouldn't, but I've seen guys reinstall a yoke and not be able to turn the new yoke with a wrench, which can burn up your bearings quick (chit happens).
I'm sure there are specifications for the bearing pre load out there someplace, though it's doubtful they will be accurate with the carrier and axles still in place. I do it mostly by feel.
The book recommends using a new pinion nut, I inspect the treads, if they are rusted out a new nut would be a good idea.