Personally I would much rather have a solid OLD vehicle that a an unfixably complex one. IMO; it is always cheaper to build what I want than to attempt to buy something less that I will always be dissatisfied with.
First determine its use then modify a straight rust free vehicle to fit the needs and to be reliable. Some of us have the skills; welding is almost always required... If that bundle of 60+ wires coming out of the computer scares you - forget it..
If you do not modify the vehicle you will, probably, be stuck with an old, or modern unreliable/less than capable vehicle.
For actual use in difficult terrain straight axles are well proven and it would be silly to consider trying to use independent suspension vehicles on the more difficult trails and unmaintained "roads". (Got and use both; there is no comparison). I regularly drive very difficult trails (some body damage likely).
My experience with Jeeps and Jeep products; because they have normally seen many incompetent owners and received little or poor maintenance along with many poorly thought out and/or poorly engineered modifications;
Is to simply strip it down and replace the power train with something newer and better. (IMO about the only "modern" things a vehicle needs is multipoint fuel injection a modern higher output alternator and perhaps antilock brakes... increased complexity means an increased likelihood of failure and often an increased severity of failure... for most a broken OEM antitheft ignition will stop it deader than a broken axle (the axle can be easily replaced even sometimes welded on the trail).
If removal of the battery means that it needs a trip to the dealer for a stupid computer reset it is a very, poorly engineered, poor choice for a vehicle, IMO.
Get rid of any full time and not low range transfer cases, and or axles that are electrically activated and install upgraded heavier duty manual versions... many vehicle differentials (especially in older Jeeps are excessively light duty and are prone to failure in very difficult terrain. Get rid of any 10 for 12 bolt or smaller/Dana 35 and or lighter duty axles and replace them with axles rated for the final desired tire size (figure on spending at least $200 per axle in scrap yards then overhaul the axles and install gears (again skill is required), optimized for the tire size for highway performance and selectable lockers. .. welding and bracket/suspension fabrication will likely be required to make them work.
Seriously consider using a manual 5 speed overdrive transmission properly rated for the engine torque; preferably with a first gear close to 4:1 (many will argue for automatics but I have had only 1 vehicle in the last 50 years that had an automatic transmission that did not fail, most needing a tow truck)... Have also had manual transmissions that failed but they always were drivable enough to get home. If you cannot drive a manual transmission properly LEARN; it will probably gain you 3 miles per gallon.
In general;
Excessively small engines tend to not do as well off road as moderately powerful v-8s; my decision point on whether to try using a particular engine off road is; if it can generate, in a broad power band @ less than 2,800 rpm, around 200 horsepower and 200 lb. feet of torque it will probably work in a properly set up mid weight (less than 4500 pound) vehicle.
Match the vehicle and equipment to the use or you will inevitably break it/get it stuck, or both through driver error.
Avoid excessive tire sizes any thing that needs more than 4 inches of lift, or body butchery, to make it fit under a vehicle is probably a poor choice.
Avoid street (all terrain) treads for the tires all the lockers in the world will do no good if the tires slide on/in the terrain.
Avoid excessive crawl ratios when you re-gear the transfer case; crawl ratios greater than the high 60s/mid 70s work best for vehicles that are very light (2,000 pounds or less).
Seriously consider, appropriately sized, four wheel power disk brakes.
Enjoy!