I assume you mean a 3" suspension lift. No point in buying 2" springs.
3" springs:
-more expensive
-you can choose firmer springs if you carry a lot of weight
-you can add spacers later to level the ride or add a bit more lift
-you can add a body lift later if you want a taller look.
-transfer case and gas tank has been raised 3", not 2" like with the spacers.
2" spring spacer + 1" body
-cheaper
-stock ride
-much more complicated install
-slight danger of popping a rear spring out under high-flex situations (you can reduce the chances of this to nearly zero)
-spacers are easy to sell later if you change your mind
-side-steps and bumpers will be 1" below the body.
-the extra room above the rear bumper due to the body lift will make it easier to fit a 33" spare.
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Chris S.
2002 KJ - staying stock (almost)
2000 TJ - 2" suspension lift, 1/2" body lift, assorted skids, hooks, rock rails, rock lights, 33" BFG MTs, custom bumper, Warn 8274
Mud Puppy's Jeep site