As a general note, avoid the GM 2.8L. It's a pretty crappy motor, even in GM vehicles. Underpowered and unreliable.

The difference between the '91-95 and '96-99 4.0L is simply the engine casting. The '96-99 engine has more webbing and is apparently stronger. However, I've yet to hear of someone breaking a pre-'96 motor where they said afterward, "Wow, if I'd just had more block strength...".

The '00-01 motor has weak heads, they tend to crack. I've not heard of previous year 4.0L heads cracking unless abused horribly.

The Peugeot BA-10/5 is a weak transmission. They are commonly replaced with the Aisin-Warner AX5, which is a much stronger unit.

The Aisin-Warner AW-4 4-speed auto is a strong automatic, lots of people are running them. Slap a transmission cooler on it and it'll run forever with periodic fluid changes. They are known for leaky rear seals, as the seal is apparently somewhat difficult to center correctly. Mine has 194k and doesn't leak.

All of these transfer cases are lightweight aluminum units. However none of them are considered to be particularly 'weak'. I believe they are all chain-drive units and should never be driven on the street in part-time mode, as this will cause driveline binding. The NP242 has a full-time capability. All allow for 2WD operation. The NP231-NP242 are more sought after than the NP207, although I don't know why.

The high-pinion Dana 30 is more desirable than the low pinion, since the drive-shaft is mounted higher for more ground clearance and less drive-shaft angle when lifted. The '96-99 D30 had stronger u-joints, whereas the pre-96 D30 either had u-joints or cv-joints (which are not desirable). Apparently the stronger u-joints can be mounted to the older D30 axle. As a note, in 84-90 the D30 had a vacuum disconnect that has probably failed by now. It can be removed simply with easily available kits.

The Dana 35 rear axle is the weakest of the bunch, most won't recommend using over 33" tires on them, and even that is pushing it. IMO it's an OK axle as long as you don't plan on dumping money into it, once it breaks or you want lockers/gears, upgrade to something else.

The '91-96 Chrysler 8.25 is a little stronger than the D35, but not by much. The '97-01 8.25 is a much stronger axle, almost as strong as a Dana 44 depending on who you ask, and is desirable.

The Dana 44 only came on vehicles with a towing package, and is highly desirable. People make treks into junkyards just looking for this axle, which will swap into any Cherokee without any real work.

Ask 50 people and you'll get 50 different opinions, although I think everyone would agree to avoid the 2.8L V6, Dana35 axles, and the Peugeot 5-speed. Some people think the Renix 4.0L isn't worth having, but honestly they aren't that much weaker than the non-Renix units and are just as reliable, possibly more so due to their simpler fuel injection system. The '99-01 has a different intake that produces more power, but also has weak head castings that are known to crack. The better intake can be swapped to an older 4.0, or if you buy one with a cracked head, the older stronger head can be swapped to the '00-01. Almost all parts on these 4.0Ls are interchangeable.

In my opinion, the only real differences between the '91-96 and '97-99 models are the interior/exterior styling changes and the stronger 8.25" rear axles on the '97+ models. Other than that, I don't think there is enough difference to really say one is a lot better than the other. I love my '93s boxy styling and non-airbag steering wheel.

Hope this was helpful.