Lots of good advice given here!! But you and/or your son still need to research what you want to do. Pssshh, took me a while to figure out if my son had a 35 or 8.25 axle (have to remember to change profile, lol). If it were me I would start with a 3" lift, far easier, less added BS.

As to 31s, IMO is right at edge with stock 3.55 gears. My son has 31/4.5 lift and empty it's ok, but any load (6x10 utility trailer) it wants to hunt between 3/4 with over passes, and Colo has bigger hills than Mi. IMO, if you regear just get 4.56. As I've seen mentioned, "Don't fear the gear"

BTW, if you don't have an oxy torch , get one, you'll need it
Lots of PB Blaster and brake clean too

 

If he's just looking for a little bigger tires and a more aggressive look, I put 2" spacers and shackles on mine to start with and ran 31's with out any problems. Mine's a '93, the new body style may need a little trimming. It's defiantly the most cost effective way to go, and maybe a good place to start to see how much he is really going to wheel it. No re-gear, no SYE, no track bar, no brake line extensions, etc. Keeps it a good DD. I was commuting about 120 miles/day with mine and wanted to keep a little gas mileage. (We just put a 2" spacer kit on my sister's Liberty) There is a noticeable size difference and it allows for slightly bigger tires. Since we go out to Moab a few times/year I wanted a bigger lift.

Now I have a 3.5" RE lift with new rear leafs. Did a t-case drop kit, no SYE. If I went any bigger I would have had to get one. My rear u-joint was binding without the t-case drop kit. Kit comes with a rear brake line, but replaced the front brake lines so they didn't pull tight on full flex. Have to get a new track bar with most 3.5"+ lifts. Add another $100 or so.

I still have the 31's, on 15" rims. The 31's make my Cherokee look a little gangly with the 3.5" lift, IMO. Picking up 17" wheels this afternoon, and going to 33" tires in a week or so. I have the 8.25" in the rear, so probably won't re-gear...right away anyway. Bushings could be better with this kit, but we probably have about 40k on them before needing any replacements.

I replaced my driver side front fender; it was dented when I bought it. About $90 shipped online. Easy to take to Macco or rattle can to paint and replace. Just a handful of screws.

As far as tires go, I put my spare on my roof rack for a long time. Unless he is doing technically wheeling in 'tippy' areas it shouldn't matter with it on the top. A rack is also way cheaper than a rear bumper with tire carrier. Plus, a rear bumper means a front bumper, which means a winch, and lights. haha. Just the way Jeep builds tend to go.

In every forum keep in mind that everyone has an opinion on what's best. I chose what was best for me and my Jeep. May not be the same for you. Everyone's Jeep is different, while I didn't need an SYE with 3.5", you may. Hard to tell you what you will or won't need.

I would defiantly second the guy that said make sure all the maintenance is done before modifying. Lift, tires, weight, etc. put a lot of extra stress on parts and anything that is on it's way out will go out. May want to budget that into your total costs too.