Ok, I have a 00' XJ with 96K auto, 4x4. The other day, every time I started the engine, it would crank right up, but when it was "running" It acted like it was running only on a couple cylinders. If I would accelerate, at times would "cough""pop" through the intake. Eventually it would smooth out. My plugs are good. Today it ran fine, I drive 105 miles a day in eastern Virginia. this problem existed before, but is not a constant problem, only once in a while. This does have the sealed ignition system.

is your check engine light on?

Sorry, No lights at all, never had the "check engine" symbol lit since I have owned it.

if you fine out what it is let me no my 96 cherokee does it to and i have tryed every thing think you.

What did you do to try and fix the "problem". We had a winter snap hit North Carolina, Jeep ran great. This is a problem that is intermitent, and equally frustating. Lets see if we can't put a list together and maybe find a solution.

egr valve?

I would say oxygen sensor or MAF sensor

But wouldn't any one of those componants cause an engine code, or engine service light? I have never gotten a lite whenit is running bad.

I bet dollars to donuts your plug wires are bad.
Wires can 'leak', that is, when the insulation breaks down, spark energy can jump from one wire to another by induction and cause the plugs to spark at the wrong time. This is more likely when the air is cool and damp and the engine is cold.
Change your wires, and if you have one, the distributor cap and rotor. I am quite confident this will fix your problem.

This was happening to me, turns out not only were plug wires bad, but I had a bad fuel injector.

I had the same thing in my 96 it was plug wires, Changed them and no more problem