Mastiff: don't worry about putting the hubs on yet, not until the axle end play is set. As Robert sez, torque the nut with the tire on and on the ground. You are correct, the torque value is 140-160 ft.lbs. You go to the closest hole/slot for the cotter pin, do not back off to find one.
Here's how I set them up:
the bearing is snapped on the shaft, you just kinda throw it on, the taper on the bearing's id lines it up on the shaft's taper. Put the shaft in the axle tube while being careful not to nick the inner seal. Then put the bearing's cup on and carefully seat it on the bearing cone and in the housing. Lightly, very lightly, tap it in place until it contacts the cone.
On the driver's side, assemble the backing plate and retainer plate and tighten the nuts. On the passenger side assemble the shims, backing plate, and retainer plate, and nuts also. As you've guessed, I've left the outer seals out at this point, we don't need them right now. With a slide hammer, jerk the passenger side axle out with a few light taps. On the driver's side, pull the axle out also; this seats the cones in their housings so you'll be able to see what the full axle end play for both sides will be. You are looking for an end play of .001" to .010". That's a pretty wide playing field to fall into, check with your dial indicator. Add or subtract shims to get between .001 and .010" after all is up to snuff, now is the time to put it together completely with the seals and hubs.
Anytime you change anything, I.e. Old with new, the setup will change also. So yes, shims can come and go with new bearings.
Have you done any work to the differential? I've read your concerns about the play in the spider gears.