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Need help with a really weird misfire

Old Jan 11, 2026 | 08:23 AM
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Default Need help with a really weird misfire

2000/4.0 got the jeep from an auction so I have no history for it.. cold start its perfect starts right away and runs fine , during warm it starts misfiring on 1 really bad and if I drive it computer suts off 1 and 6.. after it warms up (around 190) and runs there for like 2,3 minutes misfire is either going away or it almost disappears.. if I increase rpm at any point it runs fine after setting on idle starts again..the following have been replaced some of them twice just to eliminate defects.. coil ,spark plugs , cam sensor and sync shaft (calibrated with scan tool) crank sensor injector and injector wires and connector with new all the way to the computer, upstream o2 ,throttle position sensor and idle control valve, compression test its o.k (125) not ideal but not bad.. same compression on 2 but no problems on 2 so I'm calling it good.. leak down test perfect send 100psi holding 100 psi.. fuel pressure is 49 all the time.. im really running out of ideas.. add 2 grounds on the existing wiring straight from battery to engine block but no difference.. I'm currently waiting on a pcm just to eliminate the last thing I can think.. anyone had anything similar before?

Last edited by Dimitris; Jan 11, 2026 at 08:40 AM.
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Old Jan 12, 2026 | 08:18 PM
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Your PCM hunch is probably right. Those 4.0s are known for cracked solder joints inside the computer, especially causing heat-sensitive cylinder dropouts. Since you've replaced literally everything else, the computer is the last likely suspect. Swap it in and see.
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Old Jan 13, 2026 | 12:47 AM
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That's a lot of sensors - I assume the list is over time and they all tested bad BEFORE you changed them? My VOM has gotten a lot of use since I got my XJ too. Before you buy a PCM or install it ,spray the contacts with electrical contact cleaner - It's worth a try on a 25 year old plug and the spray can can set on the shelf for other uses.
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Old Jan 13, 2026 | 07:47 AM
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Originally Posted by Very Red XJ
That's a lot of sensors - I assume the list is over time and they all tested bad BEFORE you changed them? My VOM has gotten a lot of use since I got my XJ too. Before you buy a PCM or install it ,spray the contacts with electrical contact cleaner - It's worth a try on a 25 year old plug and the spray can can set on the shelf for other uses.
Nope there was replaced back to back in like 2 weeks.. I don't have a scope to actually test them.. I even considered getting one but getting it and set it and compare the waveforms to good known ones its almost impossible without experience with a scope.. so yeah I just throw parts hopping for the best.. connector on pcm was inspected it looks pretty good ,almost too good.. if pcm dosent do it I'll grab a scope and start playing with it until I learn how to use it.. and if that dosent do it I'll set the thing on fire 🤣
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Old Jan 13, 2026 | 12:30 PM
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Default No scope is required. A cheep VOM will do

Originally Posted by Dimitris
Nope there was replaced back to back in like 2 weeks.. I don't have a scope to actually test them.. I even considered getting one but getting it and set it and compare the waveforms to good known ones its almost impossible without experience with a scope.. so yeah I just throw parts hopping for the best.. connector on pcm was inspected it looks pretty good ,almost too good.. if pcm dosent do it I'll grab a scope and start playing with it until I learn how to use it.. and if that dosent do it I'll set the thing on fire 🤣
These things can become money pits - so most of us dig with our recovery shovels. Your using a back-hole. Just Empty Every Pocket is not required.

Get a shop manual - testing procedures and a list of codes are contained in a manual. A simple VOM can test the sensors BEFORE you buy them.No scope is required. This is my drill, because I'm bad at guessing - open the shop manual, take the VOM out and a cold one. If you don't have auto mechanic leads, you can use alligator clip leads to grasp push pins that penetrate the wires. You'll need jumpers to test a MAP. Assuming your air filter is clean, spark plugs, and wires are good, check for dangling wires grounding. The wires coming up from the O2 to the fuel rail wiring harness are a good place to start. Craw under your jeep and survey the wiring and the evap line. Then test your sensors: the temp sensor, idle speed stepper motor, O2, MAP, MAT, Crank and Cam PS and TPS. In my experience, the crank position sensor is good - or you stranded by the side of the road - but test it anyway. If they are good and your throttle body is clean, move to the injectors: clean them and test the resistance for each one. You can pull them and use a 9v battery to produce a click unless it's defective.


Last edited by Very Red XJ; Jan 13, 2026 at 12:32 PM.
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Old Jan 13, 2026 | 01:35 PM
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^good advice but try not to stab wires like that. Its a good way to get corrosion started.
Sometimes its unavoidable, but best practice is to use a backprobe pin and squeeze it between the rubber seal and wire in a connector.

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Old Jan 13, 2026 | 03:40 PM
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Originally Posted by Very Red XJ
These things can become money pits - so most of us dig with our recovery shovels. Your using a back-hole. Just Empty Every Pocket is not required.

Get a shop manual - testing procedures and a list of codes are contained in a manual. A simple VOM can test the sensors BEFORE you buy them.No scope is required. This is my drill, because I'm bad at guessing - open the shop manual, take the VOM out and a cold one. If you don't have auto mechanic leads, you can use alligator clip leads to grasp push pins that penetrate the wires. You'll need jumpers to test a MAP. Assuming your air filter is clean, spark plugs, and wires are good, check for dangling wires grounding. The wires coming up from the O2 to the fuel rail wiring harness are a good place to start. Craw under your jeep and survey the wiring and the evap line. Then test your sensors: the temp sensor, idle speed stepper motor, O2, MAP, MAT, Crank and Cam PS and TPS. In my experience, the crank position sensor is good - or you stranded by the side of the road - but test it anyway. If they are good and your throttle body is clean, move to the injectors: clean them and test the resistance for each one. You can pull them and use a 9v battery to produce a click unless it's defective.

just to br clear i really appreciate your response but your mistaking.. we are talking for an intermittent problem that goes away in matter of minutes.. you can definitely test completly deaf sensors.with dom but you can't fully monitor them.. for example I hear crack in a crank could make it work fine and then read bad after warm up and expand on that crack.. scope needed to be able to monitor sensor signal at the sensor and right on the pcm to be sure that everything is o.k.. on my case its just one cylinder so vacuum leaks don't apply because that would effect the hall bank plus ft numbers will be up.. it could be a vacuum leak right on thr tube on intake going to one but its not i test it.. o2 also should effect the hall bank.. injector is good tested with multiple tests.. that's why I'm saying I need ascope to be able to monitor primary and secondary, injection pulse and other sensors right on the sensors and on the pcm connector to finally figure what is missing and its misfiring..
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Old Jan 13, 2026 | 04:40 PM
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Default Thanks, I agree that stile of probe is the best to use

Originally Posted by 89Laredo
^good advice but try not to stab wires like that. Its a good way to get corrosion started.
Sometimes its unavoidable, but best practice is to use a backprobe pin and squeeze it between the rubber seal and wire in a connector.
Thanks, I agree that stile of probe is the best to use.. I've lived in the dry South West for a long time. Here, corrosion isn't as much of an issue - thanks for pointing that out
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Old Jan 13, 2026 | 04:53 PM
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Default I guess I've been fortunate

Originally Posted by Dimitris
just to br clear i really appreciate your response but your mistaking.. we are talking for an intermittent problem that goes away in matter of minutes.. you can definitely test completly deaf sensors.with dom but you can't fully monitor them.. for example I hear crack in a crank could make it work fine and then read bad after warm up and expand on that crack.. scope needed to be able to monitor sensor signal at the sensor and right on the pcm to be sure that everything is o.k.. on my case its just one cylinder so vacuum leaks don't apply because that would effect the hall bank plus ft numbers will be up.. it could be a vacuum leak right on thr tube on intake going to one but its not i test it.. o2 also should effect the hall bank.. injector is good tested with multiple tests.. that's why I'm saying I need ascope to be able to monitor primary and secondary, injection pulse and other sensors right on the sensors and on the pcm connector to finally figure what is missing and its misfiring..
I guess I've been fortunate to get buy with modest VOM for years. Sometimes, I'll find a component defective, replace it and it runs fine. Then the next morning it doesn't. I guess the PCM gets a different temp reading and that changes it's outlook on my life. But every time my VOM has been able to find another culprit. Pleas let us know what your scope tell you. All of us go through this
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Old Jan 14, 2026 | 06:39 AM
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I don't know if it helps, but these symptoms sound almost identical to when I replaced the upstream O2 sensor in my '98, and the new sensor had a bad heater element.

It would run great cold, but after a hot start it would spend a few minutes running so rough that it was almost undriveable. Once it got past that stage, it would then return to idling/driving like normal.
I eventually disconnected the O2 sensor and tested the resistance across the two wires going to the heater element, which had no continuity.

A new O2 sensor under warranty 100% fixed the problem, but I tested resistance before installing it to make sure there was good continuity!
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Old Jan 15, 2026 | 03:30 AM
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IMO using push pins protects connections better:

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Old Jan 16, 2026 | 06:26 PM
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Misfires are difficult beasts...i fought mine for 2 years before the fix. Mine was only nbr 2. It would come on at idle/ low speeds and i swore they went away at speed. Problem was that they did not go away at speed...you just couldn't feel it. I borrowed my friends insanely expensive snap on scanner that had a misfire counter program in it. It would continuously log misfires no matter what the engine speed, but would only trip the cel at the lower speeds. Im sure yours and everyone's else is really the same. . Yours gives better clues. Nbr 1 and 6 fire off the same coil pack in the rail. I see you changed the rail 2x so its not the rail but might be the harness. The entire rail is hotwired through one of the 4 wires in the connector. The other 3 are grounds that cycle based on the rotating flexplate past the crank sensor. A bad crank sensor would probably misfire the other 2 coil packs once in a while but since its always 1/6 its probably wiring . I don't think the computer has a program to intentionally misfire anything as a protective measure.
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Old Jan 16, 2026 | 08:47 PM
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Originally Posted by bluejeep2001
Misfires are difficult beasts...i fought mine for 2 years before the fix. Mine was only nbr 2. It would come on at idle/ low speeds and i swore they went away at speed. Problem was that they did not go away at speed...you just couldn't feel it. I borrowed my friends insanely expensive snap on scanner that had a misfire counter program in it. It would continuously log misfires no matter what the engine speed, but would only trip the cel at the lower speeds. Im sure yours and everyone's else is really the same. . Yours gives better clues. Nbr 1 and 6 fire off the same coil pack in the rail. I see you changed the rail 2x so its not the rail but might be the harness. The entire rail is hotwired through one of the 4 wires in the connector. The other 3 are grounds that cycle based on the rotating flexplate past the crank sensor. A bad crank sensor would probably misfire the other 2 coil packs once in a while but since its always 1/6 its probably wiring . I don't think the computer has a program to intentionally misfire anything as a protective measure.
mine is only on number 1 really bad on warm up and almost disappears after 4,5 minutes after full warm that's verified by feeling it and by monitoring live data on scan tool.. the 1 and six im getting is only when I drive during the warm up and its the pcm cutting off 1 and six (injectors) to protect the cats from raw fuel going to them.. if I pull over turn it off and on the 1 and six ( cylinder deactivation) from the pcm goes away until 1 starts missing again.. pcm detects it and shutting off 1 and six again.. i don't believe its wiring because its missing only in #1 and coil fires 1# and #6 so if that was the case it should be missing on 2 cylinders.
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Old Jan 17, 2026 | 04:11 AM
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Originally Posted by Dimitris
mine is only on number 1 really bad on warm up and almost disappears after 4,5 minutes after full warm that's verified by feeling it and by monitoring live data on scan tool.. the 1 and six im getting is only when I drive during the warm up and its the pcm cutting off 1 and six (injectors) to protect the cats from raw fuel going to them.. if I pull over turn it off and on the 1 and six ( cylinder deactivation) from the pcm goes away until 1 starts missing again.. pcm detects it and shutting off 1 and six again.. i don't believe its wiring because its missing only in #1 and coil fires 1# and #6 so if that was the case it should be missing on 2 cylinders.
I'm not understanding these points as TTBOMK Cherokee 4.0 PCM does not have the ability to do "cylinder deactivation"-- where did you get that info?

That said, if you need to get an o-scope (I use Hantek above, if you get that far IIWY I'd look at the entry level Pico) while the box is 130-200 bucks you're probably going to need 1 or 2 additional probes so you may get to 400 bucks in a hurry.

With your scanner can you generate waveforms for the O2 sensors? Do you have 2 or 4?

I would also look for intake gasket leak, the exhaust system where a crack could affect O2 sensor readings (see bj2001's saga, didn't turn out to be that but interesting read), consider leaky injector, leaky lifter, broken valve spring, maladjusted valve(s)(yes they do need to be adjusted, or at least checked if you have an unsolvable problem)(prob find it under "preload") and worn cam lobe(s).

Last edited by Dave51; Jan 17, 2026 at 04:30 AM.
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Old Jan 17, 2026 | 04:14 AM
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BTW did you clean the injectors?
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