mystery misfire issue?

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Feb 7, 2025
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I have a 2006 Jeep Wrangler with the 4.0 motor and 188k miles on it. I've owned the vehicle since 110k miles and have changed my oil every 5k with Rotella T6 10w30. A couple weeks ago, after long drives, the motor would idle rough and would throw a P0303 code. I initially thought this was a heat soak issue as the 4.0s are known to have this problem on the third injector. I replaced the heatshield, replaced the injectors, and insulated them. No difference. Recently, it has gotten a little more common. It usually throws the code after a 30-40 minute drive now, but sometimes, it runs just perfectly fine. It's very random. I tried all the little things:

-Checked the grounds and wiring
-Replaced the coil
-Replaced the plugs
-Moved injector over to see if misfire followed
-Disconnected the O2 sensors
-Checked that the third injector was getting power when misfiring with a noid light
-Replaced camshaft position sensor
-Cleaned IAC and throttle body

Still getting the misfire. I took it into a shop a couple days ago and they said I needed a new motor. Thought it was strange as it would run perfectly fine most of the time? No lack of power or anything, and still decent gas mileage (for a Jeep). They said compression was between 100-110 on all cylinders and was at 90 on cylinder 3. I asked them to do a leak down test as well and they said that cylinder 3 had 90% leakage. This is where I am confused. Would I not have significant drivability issues if I truly had 90% leakage? Wouldn't the misfire be more consistent? And how are they getting 90 psi on cylinder 3 with that much leakage? Should it not be significantly lower? They also told me they were not able to determine where the leak was coming from. I thought that this was the point of even doing a leak down test. Is one not supposed to listen for the leak?

Anyways, I don't know how well the previous owners maintained this vehicle. I ran a bottle of Rislone engine restore in hopes to loosen up any junk in the top end and drove the Jeep for about 220 miles, stop and go. i thought for a second it might have actually solved my issue. NO rough idle during that drive until I pulled back into town and into my parking garage. Then I got the rough idle again and threw the code. So I'm not sure what's going on here. I'm skeptical that I need a new engine as the numbers do not really make sense to me. I even tested the compression myself a while back and got around 170 psi on all cylinders but that was also 20k miles ago. Maybe I did something horribly wrong within that time period. Oil analysis came back from Blackstone around the same time and everything looked great.

Are my issues likely caused by a dirty engine? Or do I seriously have mechanical issues on a Jeep 4.0 with less than 200k miles?
 
When you say "replaced the coil" I am assuming this has spark plug wires? Did you replace them?

And no it's not a dirty engine.
 
I'd recheck compression again yourself and see what you get. I know I've driven a v8 with a dying cylinder and it was honestly pretty hard to tell it was down 1 unless you were paying good attention. I can see it being borderline and having enough compression to fire cool and not as it warms up, but I'm no engine expert.. How did the plugs look? All the same?
 
When you say "replaced the coil" I am assuming this has spark plug wires? Did you replace them?

And no it's not a dirty engine.

Is there no chance a gummed up valve can't be seating properly on occasion causing the intermittent rough idle and misfire? I thought a mechanical failure would be more consistent.

No wires, coil on plug. I did replace it.
 
I'd recheck compression again yourself and see what you get. I know I've driven a v8 with a dying cylinder and it was honestly pretty hard to tell it was down 1 unless you were paying good attention. I can see it being borderline and having enough compression to fire cool and not as it warms up, but I'm no engine expert.. How did the plugs look? All the same?
All plugs looked good, exactly the same, and that is what I'm going to do next. I'm also considering having another shop just look at it. I felt like the original one I took it to was too quick to condemn the engine and send me a $5k quote.
 
Is there no chance a gummed up valve can't be seating properly on occasion causing the intermittent rough idle and misfire? I thought a mechanical failure would be more consistent.

No wires, coil on plug. I did replace it.
It? How many coils did you replace? Just the one that the OBDII said was misfiring?
 
I'd recheck compression again yourself and see what you get. I know I've driven a v8 with a dying cylinder and it was honestly pretty hard to tell it was down 1 unless you were paying good attention. I can see it being borderline and having enough compression to fire cool and not as it warms up, but I'm no engine expert.. How did the plugs look? All the same?
Does your jeep have an idle air control valve? My neon runs fine cold but after warming up or during the hot summer it idles rough.
 
I have a 2006 Jeep Wrangler with the 4.0 motor and 188k miles on it. I've owned the vehicle since 110k miles and have changed my oil every 5k with Rotella T6 10w30. A couple weeks ago, after long drives, the motor would idle rough and would throw a P0303 code. I initially thought this was a heat soak issue as the 4.0s are known to have this problem on the third injector. I replaced the heatshield, replaced the injectors, and insulated them. No difference. Recently, it has gotten a little more common. It usually throws the code after a 30-40 minute drive now, but sometimes, it runs just perfectly fine. It's very random. I tried all the little things:

-Checked the grounds and wiring
-Replaced the coil
-Replaced the plugs
-Moved injector over to see if misfire followed
-Disconnected the O2 sensors
-Checked that the third injector was getting power when misfiring with a noid light
-Replaced camshaft position sensor
-Cleaned IAC and throttle body

Still getting the misfire. I took it into a shop a couple days ago and they said I needed a new motor. Thought it was strange as it would run perfectly fine most of the time? No lack of power or anything, and still decent gas mileage (for a Jeep). They said compression was between 100-110 on all cylinders and was at 90 on cylinder 3. I asked them to do a leak down test as well and they said that cylinder 3 had 90% leakage. This is where I am confused. Would I not have significant drivability issues if I truly had 90% leakage? Wouldn't the misfire be more consistent? And how are they getting 90 psi on cylinder 3 with that much leakage? Should it not be significantly lower? They also told me they were not able to determine where the leak was coming from. I thought that this was the point of even doing a leak down test. Is one not supposed to listen for the leak?

Anyways, I don't know how well the previous owners maintained this vehicle. I ran a bottle of Rislone engine restore in hopes to loosen up any junk in the top end and drove the Jeep for about 220 miles, stop and go. i thought for a second it might have actually solved my issue. NO rough idle during that drive until I pulled back into town and into my parking garage. Then I got the rough idle again and threw the code. So I'm not sure what's going on here. I'm skeptical that I need a new engine as the numbers do not really make sense to me. I even tested the compression myself a while back and got around 170 psi on all cylinders but that was also 20k miles ago. Maybe I did something horribly wrong within that time period. Oil analysis came back from Blackstone around the same time and everything looked great.

Are my issues likely caused by a dirty engine? Or do I seriously have mechanical issues on a Jeep 4.0 with less than 200k miles?
Time to retest, it sounds to me like they did not have the throttle wide open getting numbers like 100-110. The minimum compression for a gasoline to even fire is 100-120. With 90% leak down you would 100% hear it coming from the sump or intake or exhaust or blowing coolant out of the radiator or an external leak as those are the only places the pressure can go.

The last 2 are quickly confirmed or ruled out, the others you will hear very clearly.

NO rough idle during that drive until I pulled back into town and into my parking garage. Then I got the rough idle again and threw the code

It seems to me there there is a good possibility that you got a defective new part like the oil or even a plug (rare but not unheard of). I assume these are not dealer OE parts? Try moving the coil and then the plug and see if the mis follows.
 
Does your jeep have an idle air control valve? My neon runs fine cold but after warming up or during the hot summer it idles rough.
Mine does, I pulled it out and cleaned it. It seems like it is working fine. I do not think they go bad too often, and if it did I think it would cause a P0300 multiple misfire code right? Not just be specific to cylinder 3.
 
Time to retest, it sounds to me like they did not have the throttle wide open getting numbers like 100-110. The minimum compression for a gasoline to even fire is 100-120. With 90% leak down you would 100% hear it coming from the sump or intake or exhaust or blowing coolant out of the radiator or an external leak as those are the only places the pressure can go.

The last 2 are quickly confirmed or ruled out, the others you will hear very clearly.



It seems to me there there is a good possibility that you got a defective new part like the oil or even a plug (rare but not unheard of). I assume these are not dealer OE parts? Try moving the coil and then the plug and see if the mis follows.
Unfortunately it is a coil rail and just one piece, I cannot move it around. Also, it is a waste spark system so I think if that was the issue I should be getting a miss on cylinder 4 too. Swapped it anyways to rule it out. I'm going to have another shop that is familiar with these motors retest. It is very strange to me too that they cannot identify where a 90% leak is coming from. That doesn't add up to me.

If it was an engine issue, valves not seating correctly sometimes because of seals etc. would probably cause my issues right? Maybe I'll have the shop stick a borescope in there?
 
I had a strange misfire on one cylinder of my 2012 xB that I’m 99% sure was gummed up compression rings. I did a Berryman’s soak of that one cylinder and it never reoccurred. This was after replacing the plugs and coil.
 
Valve lash on cylinder 3? Maybe it’s tight? Would be good to pop the cover off and have a look. These engines can handle a fair amount of imprecision and abuse and simply keep tractoring forward, unless you like to rev ‘em.
 
I had a strange misfire on one cylinder of my 2012 xB that I’m 99% sure was gummed up compression rings. I did a Berryman’s soak of that one cylinder and it never reoccurred. This was after replacing the plugs and coil.
I think I might do this anyways, can't really hurt right.
 
Ok so I drained the old oil out, replaced with fresh oil and dumped half a can of seafoam in the crankcase. 300 miles in and no misfiring at idle. I'm leaning more towards this is a carbon deposits issue with the valves? Could just have somehow temporarily fixed whatever problem is going on though. Maybe I re do it and try changing the oil again after 1000 miles if it doesn't come back?

Also considering seafoam in the intake or maybe even spraying some water in to break whatever carbon is in there loose.
 
Ok so I drained the old oil out, replaced with fresh oil and dumped half a can of seafoam in the crankcase. 300 miles in and no misfiring at idle. I'm leaning more towards this is a carbon deposits issue with the valves? Could just have somehow temporarily fixed whatever problem is going on though. Maybe I re do it and try changing the oil again after 1000 miles if it doesn't come back?

Also considering seafoam in the intake or maybe even spraying some water in to break whatever carbon is in there loose.
Its all a guess at this point, as you still don't have a diagnosis you can trust.

If you wish to assume it is intake valve deposits, I can vouch for this product. https://parts.gmparts.com/product/a...wzWQKSlkfN_-uiAVs6Nr3Masg7oUUO2XMljw2eRUvr5_6 GM Engine Top Cleaner.

You introduce it into the intake system with the engine running and it will help to remove intake deposits.
I had a Ferrari F355 that had some uneven leak down numbers on a couple cylinders and the dealer ran this stuff through and amazingly the numbers improved significantly. I drove the car another 35k miles without issue...then sold the car.
 
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