Hey Rick, your list looks to be fairly comprehensive as far as supplies and upgrades go. If you are replacing the pinion seals, I would be prepared to check, and reset if need be, the pinion pre-load and gear lash of the diffs. It's never going to be easier than when they are out of the axle housing, might as well be proactive.
As far as your questions go:
1. It doesn't look like you are forgetting anything, but there will ALWAYS be things that pop up along the way to throw you off. Just budgeting a bit extra will help overcome them.
2. I can't answer directly about the 80 master, but a larger piston doesn't necessarily mean more braking power. Actually, it would just move more fluid at a lower pressure. That's why folks change out the clutch master for a larger one, it moves the slave further with the same stroke. But you don't need as much mechanical advantage with the clutch. I think from the factory the larger bore masters are matched with boosters that supply more assist. If it were me, I would probably go with the 60 master.
3. With the work you are planning, you will be completely going through each axle pretty thoroughly. Between dis-assembly, cleaning/painting, and re-assembly, you will be covering every inch of the axles, aside from the differentials needing attention, you should be solid.
4, Removing the axles will require removing the bolt from the spring eye (shackle end in your case), and the ubolts to free them (and of course brake lines, drive lines, steering, etc). I have left the tires on so I could roll them out from under the truck, or set them on a moving dolly, because they are pretty heavy things. But all in all, pretty straight forward to get them removed.
5, I just replaced all my lug studs so I could bolt on a set of alloy wheels (the stock studs were too short). I didn't realize just how worn the threads were on the old ones until I threaded fresh lug nuts on fresh studs, but it was a world of difference. For the $80 or so I spent on the project, I wouldn't hesitate to do it again. And a press is the appropriate way to install the studs, but it really depends on how much pressure it takes to get the knurling of the stud to seat in the hub. If you can "pull" them into place with only using 40 or 50 Lbs of torque, you aren't stretching the stud and causing it any real harm. If you have to apply as much, or more torque than it requires to attach the wheel, I would definitely use a press. I would also say that if I had the axles all broken down to do the rebuild/refresh you are going to do, I would just find someone with a press and be done with it.
Hope that helps some. I'm going to be running my rig this winter, now that I can, but I will also have to do a knuckle job on it to fix the leaking inner axle seals. I plan on pulling the front just as you are so I can clean and paint it at that time, so we aren't that far apart. I don't have to change knuckles, but the service will be about the same. I look forward to seeing the progress you make with the the old ClusterTruck.
lefty b