Body lift will have no affect on driveline angles etc. but will be alot of work to install. 2" shackle lift will affect the driveline angles and pinion angles of both axles. Probably not enough to be a problem but also will not give you the 2" of lift you may be expecting. Typically a 2" shackle lift pushes your spring down and inch and your body up and inch. The best way is to pick up a 3-4" lift kit and install it. Far fewer problems.
'91 YJ, 4.0L 5sp, Atlas II, RE SOA + 2"BDS, 35" Explorer Xterrains, ARB's & 4.56 gears, WARN 9000i