I'll try and answer some of your questions as best as I can.

1) There's nothing mechanically difficult about removing/replacing the rear axle except you will have to bleed your brakes afterwards and I'd check into how the ABS system is removed from the rear axle and brakes.
2) No idea, but I would plan on running into problems that delay you at least one day because projects always seem to take longer than they should.
3) It would be MUCH easier to use air tools, especially if your control arm bolts have even been removed and replaced using air tools. I have a LCA bolt that I can't remove right now using regular hand tools.
4) IIRC, in 99, 00, or 01 the rear end changed to 2 brake lines, someone posted recently about that switch so a search may reveal it.
5) I'd look into a guarantee, a lot of yards have a certain number of days to install a part and discover it's bad for it to be returned.
6) Have you checked car-parts.com, they have a great online search?

Misc. thoughts:

I would definitely get jack stands (may be obvious) to hold the truck up while you're working on it.

If you haven't put rear shocks on yet, now would be a good time since it will be very easy to access the top mount.

If you don't wire the e-locker immediately, make sure you tape off the plug so it doesn't get corroded by salt during the winter.

Best of luck, I hope this cures your problems. What are you going to do with your old axle?