This one seems to have everyone stumped. I have a 2000 XJ, 4.0. I was out in Utah wheeling, when my CEL comes on w/ no warning, and the XJ starts running very rough, and loosing power. Made it back to civilization, and checked the codes, which were P0300, 0303, 0304, 0353.
P0300 = multiple misfires
P0303 - misfire on cyl 3
P0304 - misfire on cyl 4
P0353 - coil pack 3 (can't remember exact wording)
I replaced the coil rail, and the plugs on cyls 3&4. Cleared the codes, and it ran file for a 5 hour drive from Moab to Granby, Colorado, except for a brief period right when I was shutting it off as we made a stop. At that time the CEL came back on, and it ran rough. After leaving it set for about 15 mins, it fired up and ran fine for several more hours.
In Colorado, codes came back, along w/ all the symptoms. I had to get it back to Michigan, so I put in another coil, and two new plugs. Ran fine for about 15 min. I did this just in case I had gotten a bad coil.

Took it to a shop, and the mechanic seemed to be be very knowledgeable, and had a 97+ XJ himself. He said it was the camshaft position sensor. Put that in, and headed home to Michigan. About an hour away, it started doing the same thing! Decided to just keep going and risk it. Made it home OK. Whenever it started running rough, I would just shut it off, and restart it, and usually the first or second time I did that, it ran smooth.

So that's what I've been doing. If I'm going down the road, and it starts running rough, I shift into neutral, turn it off, restart it, and it generally runs much better, though still a slight bit rough.

Any idea what the issue is? Appears it's not the coil, plugs, or camshaft position sensor.

 

Heat soak maybe? Is it 00+ or 01/02 that have the weak head? If so don't they like to crack between 3-4? This may sound strange but check battery, cables, connectors and alternator. My wifes had a misfire and o2 code, I replaced both o2s and the code went off for a while then returned. Then I replaced cables with 2 gauge, connectors and put a v8 zj alt(stronger) in and the codes disappeared and the rough idle and long cranking went away.

 

Thanks for the input! Anyone else got any ideas?

 

Did you replace the boots you have to replace them .

 

Do you mean the boots that go over the plugs? Those were attached to the coil rail that I got, so they couldn't be replaced individually.

 

Weou09 has a good point, 00 and 01 have the 0331 head casting that cracks between 3 and 4.

 

Took it to a shop today. They tested it and said that the signal from the powertrain control module to coil pack #3 is inconsistent. This would explain why sometimes it runs well, and sometimes not. Also, this is what a friend who runs a Jeep dealership service dept suspected as a possible cause.

 

Good to hear! Glad it wasn't the head...

 

I have the same problem, did you replace the PCM and did it fix it?