Areas of concern:
- Get to know your TJ as it stands now. Add as little weight as possible. Keep the rpms near stock to get best street and offroad performance.
- Want an auto to keep the tires spinning in the mud and not studder like shifting gears with a manual. Add larger tranny cooler and change the stall speed of the converter via replacement.
- Wheels and tires. Keep them skinny and knobby if you want mud.
- Axle(s). 8.8 swap or better yet a complete matching front/rear swap. Look for a full floater rear axle. These would come stock in 1-ton applications and are hefty big. You could look for a semi float rear axle with a flanged axle shafts, ie 9" Ford. So tire size needs to work with the type of axles you get. Same for the wheels. Bigger axles means bigger brakes to handle the larger tires. May need to step up the master cylinder also.
- Gear/Locker. Mud requires tire speed. Deepest gear set to work with streetable manners is best. Lockers, cheap rear locker is the Millermatic where you weld the spider gears to the side gears. For the front, LR, Aussie, those which replace your carrier gears are cheap enough.
- Suspension. Matches axles. If keeping stock axles, you could use pieces of used aftermarket components to gain necessary lift and links. You could look at doing a coil arm front suspension with a leaf rear suspension. Leaf rear requires a traction bar.
- Safety. Bumper pull front and rear would be necessary. Full roll cage. Winch as mentioned and mount.
So, here is what I suggest as a plan -
Keep it light and near stock vehicle for easy part replacement. Replace rear axle with lug pattern matching axle (ie. disc'd 8.
, add YJ leaf rear suspension SOA, rear traction bar, keep short arm front, add coil spacer in front with taller coils to match rear height, adjustable front track bar, ZJ tie rods as they are larger than TJs, adjustable front lower control arms keeping uppers stock , matching shocks for lift, YJ front brake lines (3" longer than TJs), 1-2" body lift, motor mount lift, flat belly pan, front roll cage, better seats, remove rear seat, 35x10's on 16" rim with proper offset. SYE if necessary as it's not a requirement with the TJ if rear ds breaks. The tcase is not sealed by the rear ds. If you want more tire, trim the body to fit, add bump stops to protect full compression. Add properly mounted front and rear bumpers with tow/pull points. Gear it as necessary for tire height, lock it with leftover money. Get some 3-4" wide 20-30-50' straps. Get a winch kit. Practice winch safety.
There is a lot to weigh in to making a decision to fit what where and when. Gearing is necessary for taller tires, taller tires is usually the start and are not cheap, wheels add expense, then axles, suspension, driveline. There is a lot to consider when you want to build and build once. A lot of people try to pride themselves to building once, but some never start. When they do, they are surprised on the outcome of all that is involved.