I'd suggest a re-evaluation on the purpose for doing the mods. You may want to step up in tire size to compensate for the costs of regearing. Adding larger tires should influence rear axle decision. If keeping the smaller tires, better add skid plate protection for driveline (oil pan, trans), gas tank, and body to your list. You also may want to add front/rear recovery points with the added winch.
If you keep the smaller tires, keep stock gearing, and want to minimize underneath damage, you may want to skip the spacer lift for a 1.25" replacement body spacer (body lift). This is a benefit of different sorts. By adding a small body lift, you gain space under the floor. You can then look at raising the engine and trans mounts. Engine lifts are common now for the Wrangler with the body lifts and the purpose is for driveline vibes with up to 4" suspension lifts. Lifting the trans is nothing short of providing a flat belly plate. The stock crossmember plate is a hinderance for the short wheelbase Wrangler. Another location of plating you may want to do is the steering box and the lower control arm mounts on the front axle. Installation is a little more labor intensive compared to the spacer lift, but the benefits, I think, add up more with the clearance under the center of the Jeep. Don't forget the gas tank for better skid protection.
Rear axle - usually any money spent into a stock Jeep D35 is throwing it away. This stock rear differential is timid at best offroad, carrying weight, etc. in stock form on a Jeep Wrangler even with stock size tires (depending on the driver of course). Aftermarket can provide acceptable solutions to the main problem with the stock D35 rear axle. You could keep the D35 and mod with aftermarket upgrades or swap out for another acceptable rear axle (TJ D44, Explorer 8.8, etc). Keeping the axle and adding upgrades requires equally costs in aftermarket upgrade support in shafts and carrier/locker case. Swapping another axle can be simple or require further mods with welding brackets, brake lines and ds adapter, etc. The Jeep Wrangler D44 is a total bolt in and may require no work with matching r&p. The Explorer 8.8 will require welding brackets and possibly matching r&p. Matching the front r&p to the replacement axle is probably the best thing to do with looking at upgrading to 31's or bigger tires.
R&P - Figure what r&p you will need with the 31's. Stepping up to a ratio ~10% difference is not cost effective. Will 31's be the tallest you will go? Probably not.
Lockers - viable options, manual or automatic. Manual lockers (air or cable) are just manual spools tieing both axles together. Once locked, the axles will have the same rotational speeds. Automatic lockers will allow variance in axle speeds with locking/unlocking. If you are going to change R&P, additional costs would be to add lockers. However, like other aftermarket options, you can add lockers without changing R&P and save lots of money. Lunch-box lockers (Aussie, LockRight, Easy-Locker) and cheap enough and easy enough to install and remove. You simple replace your spider and axle side gears with the locker discs within your stock case. Costs are usually under $250/new and install in about an hour. If you don't like, you can remove and replace with your stock side/spider gears.
Lift - To fit 31's on a TJ does not require a lift. You may have to adjust the bump stops as well as have different traveling shocks to make room for the 31s with a stock suspension. The 31's will fit on a stock TJ with 7" or 8" rims, depending on the actual backspacing of the rims. Getting the spacer lift and matching shocks will do a lot for the suspension. Some spacer lift kits provide bump stop risers and/or longer bump stops as well as a rear track bar bracket. Risers are simply a block on the axle secured with a bolt. Front axle requires a self-tapping bolts due to having no access to underneath the plate on the passenger side. The track bar axle mount limits the access to underneath this mount. Rear axle coil mount, you have ample access to place a nut under the mount to hold the riser in place.
By adding a spacer lift, the axles will be pulled to one side of the vehicle. This is done by the track bar. The track bar maintains the axles under the vehicle. At static height, the axles should be centered under the frame. Any sag/lift from that point, the track bar pushes/pulls the axle to one side from the frame mount. Depending on the wheel's backspacing and tire width, you could rub the frame on one side during suspension cycling. An additional upgrade to the spacer lift would be adjustable track bars. Most complete kits will provide a rear track bar bracket. You don't want one for the front as you want the tie rod and track bar to follow the same angle and be horizontal as possible to minimize bump steer.
Another potential problem with the TJ is the retention of the coils. With enough travel in the shocks, the coils have been known to fall out. You should look into some kind of coil retention for the springs.
In addition, with a spacer lift, the rear shocks change their angle. With the cycling of the suspension, the shock body may rub the lower coil bracket on the rear axle. There are offset brackets to help make the shock clear. This also depends on the shock's overall body width.
Front sway bar disconnect - The aftermarket has many viable options to choose for the front sway bar disconnect. It all depends how dirty you want to go to disconnect or reconnect. TeraFlex S/T bar system is one of those options. Their website should tell you if any mods would be necessary for install and use. From what I can find, its a simple bolt in/replace with their hardware kind of install. Disconnecting/connecting, you are rather clean also.
Tires - TJs come stock with 30s and 31's are not that much bigger. Keeping the 31's on the stock rims would help maintain the tire under the flare. Many tire mfrs tires are not true to the nameplate of the tire. Your 31's may be under 30" mounted.
Winches - Winches are a different story. In choosing a winch, as well as its performance, mounting the winch is another consideration. Superwinch has a reputable name for sure. Add to the winch, a winch recovery kit and several varrying length straps. Going with a nylon rope rather than wire cable has benefits as well as losses. Weight, safety and reusable/repair are all benefits. Tearing is a loss. However, if you are not consistentaly tearing up winch cable, then its minimal.
On-board air - There are many options in this topic. You can look at the non-portable setup, mechanical or electrical. You can look at the portable setup, electrical or rechargable. CO tanks appear to be well used but do require refill. I have a non-portable Viair setup with a tank. The tank is the best thing for OBA, but consider the system and its performance that makes the system work as a whole. My tank is mounted opposite the muffler. My Viair is the 450C and is mounted under the master brake cylinder.
Bumpers come with options for grille protection/winch/light/recovery mounts up front and spare tire sway away/cargo trays in the back. Getting a built in hitch frame for the rear bumper requires the bumper mounts to be strengthed at the frame. Some front bumpers protect the steering box with an integral plate. All viable options for a Jeep.
Wow, I had to resign back on twice while writing/reviewing this....lol
TJ Wranglers are the easiest and most expensive Jeep to mod to the DIYers. J-E-E-P it.
