Above makes sense, but if your keeping the TJ short WB, then stretch it a bit, the wheelbase that is. If your staying with stock axles, if you've got that dana35 get rid of it, go 8.8 or dana 44. The front change to an HP 30, then regear the axles... depending on tire size. I would looke into a tranny swap and eventually upgrading your 231 t-case to a HD version with slip yoke... Your really openning a can of worms at 35" tires. Your axles, suspension, steering, brakes, will all have to be upgraded to have a dd trail rig. I don't know what your budget or time schedule is, but on the cheap (and it still isn't that cheap), this is what I would do...
-change the rear out to a Ford 8.8 with the disc brakes out of a '95 up explorer, the front to a HP dana 30 out of a little cherokee.
- The HP 30 would add the warn hub kit, chromo axles, 760 joints
-tires 33's with 3.5" back spaced 15x8 or 15x10" wheels, adds width and stability
-Regear to at least 4:88, your Jeep has 4:10's now
-stretch the wheelbase an inch or two
-cold air intake, and exhaust upgrade, HF cat, free flowing mufler. That engine is plenty strong enough to handle that weight, and trailer tow 2G's
- do a low lift, run tube front fenders, and cut the rears and add steel flares. Low CG is important for a dd and trail rig, especially towing
-run some adjustable shocks like the Rancho 9000 to set your load and towing abilities to max. control
-sway bar dc's or better the currie sway bar set-up
-Currie steering minimum, or an OTK set-up with ton TRE's
-extended brake lines, upgrade rotors, and pads at least...
An engine upgrade like a 5.9 is expensive, and I really don't think necessary for towing 2G's...
If your set on an engine swap, call the Nashville, TN 4 Wheel Parts store on Nollensville road, and ask for Sam. Only Sam there... He's done a bunch of engine swaps, including a 5.9L into a TJ. He can give you an idea if 1- it's worth doing 2- The cost.