Ok, not in order, by any means.
I've don't this twice, myself. The first time, I bought Timkin hubs which had new studs. The second time, I only replaced one side, and didn't get studs. I support the assembly on blocks and pound out the studs. A lugnut screwed onto the end takes the beating and prevents the stud from being mushroomed.
Putting the studs back in: Once I asked a shop to do it, and it was done with an air hammer. When I did it myself, I used a lug nut and a couple of greased washers to pull the stud through after getting it started from the back with a hammer..... with everything supported to the bearing wasn't getting beat up. A couple of studs didn't really get seated until the wheel was back on.
If re-using parts make sure all rust and dirt is gone. I used a wire cup on a angle grinder. I still had to re-do one side as runout, as checked with a dial gauge, was out of spec. I apply antiseize to all mating parts so they aren't stuck the next time.
Removing the hub from the knuckle: The last time, I had one side I had to beat out, and the other basically fell out. I think I pounded on the loose bolts from the back. I've heard that the Dodge guys will use and extention wedged in between the hub and something solid and push them out by turning the wheel. I'm not sure if that would work on our trucks. Those 4 bolts are availble from GM and Dorman.... they're not that expensive. Replace them if they are questionable at all. Make sure you can get the socket fully seated before applying torque while trying to remove them.... maybe tap the socket on with a brass hammer after scrapping out any crud from around the bolt heads.
I have not used any kind of puller, just hammers applied with caution.
I use anti-seize on all threads after cleaning them with a wire wheel.
I test lugs being re-used with a known good lugnut, and then tested each lugnut, making sure I had 16 of each..... I had extras of both saved.
My 99 manual doesn't really describe this eithier. It basically says "remove rotor", as if it were a 1/2 ton with slip on rotors. The drawings are horrible and the manual edited poorly.
I have re-used spindle nuts, and not had a problem. The first time, I think I used anti-seize on them so they wouln't get so stuck, and also to lower the torque requirement, as the torque spec is quite high.... higher than any torque wrench I have available. This last time, I may have used Loctite, but I don't recall for sure. To remove the nuts initially, I used heat, penetrating oil, and a breaker bar. The last time, I had to use an impact.