Start off adding the basics, brake lines and e-brake cables, then measure for new shocks. After that just drive it and see what it feels like, then add anything else that you might need.
I was at 2.5" and added longer shackles and spacers for another 1.5" and never had to drop the t-case. I didn't extend the brake lines or the e-brake cables, but sometimes God watches after fools! I'm in the process of changing my rear dif to a Dana 44 and adding a RE/DPG 5" suspension lift. When I took the rear wheels off after it was on jack stands I discovered that the "limiting straps" on my rear end were the brake lines and cables!
Hope that helps,
Robert