Jeepinrob,
From what I have picked up over the years reading
and being the owner of a 88 XJ Pioneer is that the XJ that most of us have grown to know came in out in the 1987 Model year. This was the first year of the 4.0 fuel injected engine, the AW4 transmission, the NP 231 and NP 242 transfercase. I will admit there were pains with the manual transmission.
There is a distinctive difference in the 87-90 XJs because they had the Renix engine control. Things like fuel injectors, throttle position sensor, crankshaft position sensor are not common with the later XJs and with age the price either goes up or they may not be available. This series of XJ does have a knock sensor, which the later XJs do not have, which allows you to run 87 octane and not worry about knocking. As the owner there is no way to pull any error codes, you need the snap on reader or the dealer reader.
The 91 and later 4.0 XJs have the chrysler engine control which allows you to pull error codes but lacks a knock sensor. Seen posts on here people saying they have to run 89 octane to prevent knock. In 2000 they came out with the coil on plug ignition and some people say to avoid it.
The 87-90 4.0 engines are commonly referred to the non-HO engines since the 91 and later were advertised at the HO engine. The difference is the cam used, I read they traded off low end torque/power for higher HP for the ad brochure but someone may know more than me.
Chassis for the most part is the same from 84-96 and 97-01 were different from the earlier, the tell tail sign if the tail lights.
All the XJs had the Dana 30 front axle but depending on the year you could have the Dana 35, 44 or the Chrysler 8.25 axle.
I am not sure what you mean by the drive system problems were before 91 unless you are talking the manual transmission. Now there are countless posts on here about how the composite rotors warp. I know my 88 XJ has solid rotors, I think composite rotors were a chrysler "better idea". I plan on keeping my XJ because of the rotors and it has a knock sensor.
If you are looking for the triangle vent window the earlier XJs had them, not sure when the fixed triangle became the only way you could get an XJ.
I think most people think of a 4.0 power when you say Cherokee, with that in mind the 87 was the first of the breed and every following was just refinements on the 87 XJ.
Martin