First off, did the car throw a check engine light. If it is misfiring consistantly in three key cycles it will throw a code. If that is the case then you need to either buy a code reader, which I would recommend or go and have the code read at a shop. If you don't have a check engine light on then you can probably rule out a misfire do to fuel or ignition.

 

Heat soak also called lay in heat is caused by the fact that the cooling system is no longer cooling the vehicle therefore the residual heat in the engine from when it was running is now "soaking" in to the block and other components. On the '99 through '01 XJ's this superheats the fuel in the number three injector and thus causes the fuel in that injector to vaporize, in turn causing the vehicle to misfire on cylinder number three for about 30 seconds or so until the injector clears out and runs liquid fuel once again. The code that will show up in the computer is P0303. There is not much you can do for this condition in the '99 through '01 Cherokees.

 

you need to check the compression because you may have a crack between the number 3 and 4 cylinder. common on the 2000 models

 

OK, after driving the car for a while the Check Engine Light came on. P0300
p0303, and p0305. the coil and the plugs are already replaced. what els could it be?

Thanks

 

P0300 is a random cylinder misfire, P0303 is 3rd cylinder misfire, and P0305 is cylinder 5 misfire, so all in all you have a random cylinder misfire condition. You could have a cracked head as mentioned by a previous poster, have you been losing oil presure at all, even a little bit? Have you inspected the oil to check for intermix (coolant in the oil)? The problem is with the crack that can develop on the '99 thru '01 Cherokees is that sometimes it is less of a crack in the head and more of a fissure that only opens up very slightly when the engine is at temperature. Then when you shut the car down the material in the head contracts thus concealing the fissure making it undetectable in a test. I have had this happen to me and it was a fricking circus to try and figure out what was going on. I finally just drove it another 15,000 miles until I saw intermix and did a new motor. This might not be what is going on with your car nessearily but anything is possible. If I were you I would try new spark plugs and make sure the coil packs are seated properly as mentioned before. If that doesn't do it then check for vacum leaks with a can of starting fluid by spraying the fluid in short bursts at the mounting surface of anything in the intake system while keeping it away from the air filter. Also shoot the fluid at the base of any vacum lines. If you find a leak the RPM's of the engine will increase. Try that and let us know what happens.

 

Very interesting... it is happening in my '96.... I have a 2000 intake manifold.
Thanks for the explanation.