I need an 8 3/4 lesson. Better late than never!

If I put it in and set backlash I should be good right?

Check the backlash before you disassemble it, and set it back to that setting assuming this is a used R&P. If you set it to factory you 'might' get some howl (gear pattern will be off from it's wear pattern).

If you are running the roller bearings leave the thrust buttons in there. If you are running the Green bearings you can remove it. Very easy to do on a clutch type suregrip.

Also, you stated you had to tap the axles, that's because (most likely) the two sets of splines weren't lined up. There are 2 sets of splines for the axle to go into on each side.

I usually mark the bearing caps and put them back on the way they were. Don't forget the ring gear bolts are left hand thread. When you put them back in I would use a drop of RED Locktite on them and torque to spec.