- Around 96ish I believe the internal ribbing on the engine was improved to make it more rigid
- 99 got an improved intake manifold to improve performance, but also more emissions which took back some of that performance
- 99 or 2000 got the coil packs
- some bad castings for the heads, as mentioned before
- 91+ had the good (NOT Renix) fuel injection systems
- Somewhere around 99 I think there was a problem with heat soaking the injectors, causing hard starts. There was a fix for this
I'm sure there's a ton of other stuff people will chime in about
Overall, any 91+ 4.0 is a darn good motor and good for a few hundred thousand miles. Just make sure the last owner took at least slightly good care of it. I bought a 97 4.0 that a previous owner installed a 160 degree thermostat in and then drove lots of short trips with, so the motor never heated up and carbon built up inside to the point an intake valve is sticking... so now I have to pull the head. I have two other Jeeps with 4.0's, one with 200K miles that run perfect.