May Be Overthinking Things

As noted, shims are frequently used on the rear axle to correct pinion angle following the installation of a lift kit. Front pinion angle is less critical as 4wd isn't used as frequently at highway speeds. As long as the hubs are unlocked and the t-case is in 2wd, the front driveshaft doesn't spin for road use. On modern Jeeps, without locking hubs, it is more important to balance the front pinion angle and the caster as the front d-shaft is always spinning.

Mike

 

With a 2.5 inch lift kit, you shouldn't have to change anything.
As for disk brakes, go disk now....its the easiest time. At the bare minimum do a dual cylinder MC and the 11" drums should be more than enough.
FWIW, I had only 10" drums on my jeep, and went through a few puddles on a trail ride. After that, every second I was trying to stop was scary. And that was going downhill at 5mph