We don't think you can do...
We don't think you can do better than a '97-'99 Jeep 4.0L in terms of power, reliability, and ease of upgrades. The 2000 models did away with the distributor and plug wires for a coil-on-plug arrangement, but it's a good system and has proven just as reliable in the field as the old-school, cap-and-rotor ignitions.
The biggest departure from the Jeep's CJ and YJ utility vehicles in the past was the introduction of coil springs at each corner. The axles are located with a four-link control arm arrangement that uses track bars front and rear. They can be easily lifted with coil spring spacers or longer coils, upgraded with long-arm suspension links, and converted for use with coilovers depending on how gnarly you want to get with your project. Although most coils don't offer a progressive spring rate like leafs, any TJ will seem like you're wheeling on a pink, fluffy cloud. The factory control arms have rubber bushings that can wear out and get a little sloppy over time, but most of the better short arm aftermarket lift kits include new adjustable arms at least on the upper or lower side.
Check When Purchasing:
•Bent, broken, damaged control arms
•Worn, sloppy bushings
•Movement or slop at the track bar when turning the wheel
•Clunking when driving
Rubicon & Other Trim Levels
In 2003 the Rubicon model was introduced and turned the enthusiast market on its ear. The Rubicon offered Dana 44 axles front and rear with 4.10 gears and pneumatically-operated lockers (open/locked front; limited slip/locked rear), 31-inch diameter 245/75R16 MT/R, and a NV241OR T-case with a burly 4.0:1 Low and a fixed yoke on the rear. Additionally, the Rubicon offered diamond plate rocker protection, slightly larger and wider fender flares, and overall more options and amenities than the standard Wrangler or Wrangler X models.
Front Dana 30 and Dana 44...
Front Dana 30 and Dana 44 and rear Dana 44 axles are pretty durable, but the Dana 35 rear found in all four-cylinder and most six-cylinder TJs is a potential problem area. Anything from broken pinion or ring gear teeth to worn bearings to broken axleshafts are possibilities, so if you're not planning on swapping, take your time and pop the diff cover to be sure.
Another cool Wrangler came on the scene in 2004 1/2 as the 103.5-inch wheelbase Wrangler Unlimited. The LJs, as they've been dubbed, featured the same drivetrains as the TJs, but were only available in 4.0L models with auto transmissions for 20041/2. In 2005 you could get the auto or manual, as well as the a Rubicon LJ for the first time. The standard LJs got the Dana 30 front and Dana 44 rear, while the Rubicon LJs naturally got the same locking Dana 44s as the TJ Rubicons.
Otherwise, Wranglers could be optioned with any number of trim level, top and door configurations, and amenities. The four-cylinder models are considered base SE models and could be had with A/C, but mostly they're going to be lower-end vehicles with more Spartan interiors and austere exterior features. The Sport and later the Wrangler X models piled some popular options onto the SE platform without going all gonzo like the blinged-out Sahara models, which offered every option under the sun, plus exterior stuff like color-matched fender flares, side steps, A/C, intermittent wipers, cruise, and on hardtop models things like rear wiper and defrost options. Nowadays these extra options just add a bunch of weight and the potential for something to not work right, so savvy shoppers looking for a buildup project may smartly save some coin with the SE, Sport, or X models and skip the Sahara.
As for tops and door options, know what you want before you start shopping, because even used top and door assemblies fetch a premium. Hardtop models are nice if you do a lot of road driving, but they're difficult to remove by yourself and take up a lot of room to store. Soft tops are a better option if you plan on open-air wheeling. Many TJs have hard half doors with soft, removable uppers, but the full hard doors with roll-up windows offer a higher level of quiet and convenience, yet are still easily removed for open-air driving.
Check When Purchasing:
•Faded or broken black plastic fender flares
•A/C and HVAC works
•Top rips and zipper door/window functions
•Signs of water damage under carpet or rust on floorboards in early models