Search here or Google and start reading your tail off. Since I did this with Scout axles I will give you my brief .02.
Ditch the drums and swap the rear over to disk brakes. You need to cut the center section of the old backing plate out and use it to retain the axle shaft. There are several rotor/caliper variations out there. I used rear import calipers (88 Trooper) andfront Suzuki Sidekick rotors. Hand fabbed brackets for the calipers that attach to the two top backing plate bolts. There's a little more to it, but a little reading will cover the rest.
Stock Wrangler springs flex very well, but will start to sag. I am currently using 2" CJ springs, but need to change the fronts to Wrangler springs. To prevent axle wrap you can build a hop stop bar (searching will bring up many options). I used one for a couple of years, but space between the frame rails is at a premium and I and only running a six cylinder. So last winter I removed the hop stop assembly and now run seven inch long spring perches. I have not had any spring wrap issues.
Shackle reversal the way I understand and would do it. If running flat or mild lift springs, leave the shackles in the front unless you really need to keep them out of harms way. If your running 4" lift springs, the shackle reversal will help smooth the ride. Reversing the shackles changes how the axle moves when the tires contact a bump or obstruction. Instead of pushing the axle into and over the obstruction, the axle is now allowed to move backwards towards the shackle, relieving the abrupt push into the obsticle, but may result in less force/traction applied to that object to clear it.
If you have the Bronco D44 outters, swap them on. They are stronger than the Jeep/Scout design. You will need a combination of GM, Ford and possibly Jeep parts to make things fit, especially the brakes. Search... this had been covered very recently. You may be able to get by with a fabbed up drag ling and tie rod. If you have the cash, do it right once and install hi steer. I am in the process of doing this now. Again it's a mixture of parts and research will result in several different resources and ideas.
I run 35's SOA with the mild lift springs and just over an inch of body lift. I didn't think I would rub, but during a CO trip last year, it bent the rear edge of the passenger fender in ever so slightly. I would say you should be fine... with the possibility of some minor rubbing, but not resulting in damage.
I like the Scout axles. You need to cut a flat spot in the top of the pumpkin for the spring to sit. I also took the extra time to grid the wweld for the knuckles down, rotate more caster (or camber I always forget) into them and re-weld. Scout axles come with very little if any caster. You'll want about 6 degrees to have it drive nicely. If you do this, set your drive shaft angle and spring perches first, then set the knuckles. Also so this with the weight of the Jeep on the suspension/axle. I do not have a CV drive shaft. Most everyone else who does this ends up needing one. I guess I am lucky... and have a very short drivetrain. Brake lines and shocks will have to be longer and you'll probabaly have to build shock mounts.
That's the main stuff I can think of now. Keep searching... use different keay words... there are tons of articles out there and in here.