Not knowing the condition of rust on your frame, You could pressure wash it to get all the dirt, grease and oil off everything. Then go to town with a grinder and wire wheel. But that would be a WHOLE LOT of wire wheeling. might be better off having him sandblast it and then there are several paint options that you can do yourself.
This of course assumes that either there is no frame rust repair, and you can just paint, or you can weld and fab the parts to fix any rust.
As for shackle lift. Ya, it's an easy cheap lift, but too much shackle lift is frowned upon due to changes in pinion angles, suspension geometry, Steering geometry and added body sway that shackle lifts cause. Body lifts are also cheap, but dear god, do not do a 3" body lift! one it looks goofy as hell, and you also have to factor in anything that connects between the frame and items mounted to it and the body. i.e. Fuel filler hoses, Wiring, Shift linkages, Steering shaft, brake lines and the list goes on. When it comes down to it, a simple leaf spring suspension lift is the least headache.
from my experience, a simple 1" body lift and some 31's is a nice look, ride and capability for riding around town and simple trail riding. as soon as I went bigger with my CJ5 I had. I spent less time in it than under it or sitting in it making vroom vroom noises in the yard.