I would just go with the 3.5/3.25 suspension lift. In my opinion 3.5" susp lift is about as far as you want to go before you need to start changing things, angles, arms etc... I was told that body lifts up to an inch are ok but after that the Jeep will tend to get squirrely and things start to need to be modified/changed.
I have a 3.5 suspension lift and nothing had to be changed.
2000 Sahara,33x12.50/15 Bigfoot XT's,Front & Rear Limited Slip Diff's, 9500lb Warn Xi Winch, Air-raid CAI, 4" Susp. Lift, sway bar suspension disconnects, Pro-Comp ES9000 shocks all around, Full roll cage, M.O.R.E. off-road steering box brace, Rear "wilderness" brand rack with tire, fuel cans and jack carrier with bumper, Warn front Bumper/Fender flairs, , Pro-Comp windshield lights, Hard/Soft tops, Smittybilt "C.R.E.S." cargo restraint system, CB, ...blah, blah, blah...