Stutter / Misfire - No Engine Codes, Running Out of Culprits

Hi everyone, I held off as long as possible to post by using all the great resources but am now looking for those with more experience insights. This is a long one so hang in there!

Background: 2006 LJR, 6MT, ~119k. I purchased it in Sept. 2023 and have been slowly working through all the maintenance and refresh items. I'm not 100% sure when the issue started. I don't recall hearing it when first purchased. The first time I noticed was in November while idling next to a brick building waiting to plug in for inspection. That prompted me to spend time outside of the Jeep and it's much easier to notice/hear.

Symptoms: There's an intermittent misfire/stutter noise from the exhaust. It's not noticeable during cold start but I'm fairly certain that's because the higher RPMs mask it. Via scan tool, when it stutters there's a definitive dip in RPM (15-30) that causes a slight vibration and the noise. It's intermittent in that it could go 10-20 seconds or it could do it almost constantly for 10-20 seconds at a time. It doesn’t really introduce any drivability issues. It’s not noticeable other than idle (Though based on the scan tool I believe it still has the RPM variation).


I'm going to try and break what I've done and what I think I have left by the general vehicle system so they're not in chronological order per se. I also did these more or less 1 at a time to be sure to not introduce multiple variables.



Video on Youtube. Ignore the knocking sound in the beginning (that’s my son smashing something with a hammer). Easiest to hear from :20 to :27. Again, it’s a chuffing type sound



Ignition:

• New spark plugs – tried both the Autolite and Champion recommended here (gapped properly) – no change
• Coil pack – replaced with Viper style – no change
• Ran Seafoam – no change
• Battery is ~8 months old

Fuel:

• Pressure tested system and all in spec. Didn’t see any major fluctuations during idle
• Injectors – ohm tested originals and were OK. Replaced anyway with rebuilt 4 hole - no change. Noid light tested and all appear to be getting the proper signal – no change
• Ran fuel treatment for a tank – no change

Vacuum systems/leaks:

• I spent a quite a bit of time smoking everything and didn’t find any vacuum leaks. The one place I got smoke was around the throttle body butterfly (Where it spins). I followed the process for removing and replacing the o-rings. That made a significant change with only a slight leak when building full smoke pressure on the intake side of the butterfly and butterfly closed. No change to symptoms
• I found my vacuum reservoir was somewhat collapsed and cracked. Oddly enough all my HVAC controls worked. I still went ahead and replaced the vacuum reservoir
• PCV – I never had any smoke leaks via test. However, I could hear a high velocity air noise from it. I replaced the line on the rear of the valve since it was partially collapsed – no change. I also swapped in a new replacement gasket and PCV elbow. Same noise. I’m assuming that’s just the air moving through the restricted orifice. collapsed under vacuum

Sensors:

• IAC –
  • Cleaned via Jerry’s process – no change
  • OEM replacement – no change
• TPS –
  • OEM replacement – no change
• MAP –
  • cleaned only – no change

Exhaust : Replaced after purchase to comply with state (added muffler)

• O2 sensors – replaced all 4 with NGK recommended on the O2 sensor thread – no change
• I pressure tested the exhaust system (vacuum blowing into exhaust) and soapy water
• Reasonable leak at final bend at rear axle (slip fit connection). Tried new clamp but no luck. Not sure if this would have an impact?
• Small leak where single/downstream cat connects
• Small leak at exhaust manifold and pre cats connections. I tried to snug up these connections but couldn't eliminate it

Wiring:

• I’ve been cleaning up/replacing wire insulation. I haven’t found anything that looks to be an issue
• I read about the wiring that runs across the back of the engine. It looks OK but in that it’s not worn through the tape/loom. I can pull it though and double check

Engine:

• Compressions Test – good (all right at 180)
• Leak down test – good. Some very light from the valve cover via oil fill cap. Some very light from the exhaust with hear to it and complete quiet. Gauges read OK for leak down. I had read that a sticking exhaust valve could cause the chuffing sound but based on the leak down, all good. Or if it’s intermittent could it still be a cause?

General troubleshooting via scan tool:

I’ve tried to spend a bunch of time to see what I can monitor that would help troubleshoot the problem. I attached some pictures showing the RPM dips and some other readouts. What I’ve seen/paid attention to:

• RPM – visible drop in RPM when the stutter occurs
• O2 voltage – from what I can research and my limited knowledge they appear to be behaving as they should. I’ve really only been paying attention to the upstream sensors
• MAP – I’ve been looking to see if this has strange signals since it’s a sensor I haven’t replaced it. When I get a BAD stutter, the MAP signal does change
• When a major stutter occurs photos show examples):
  • MAP will increase (for example 40 to 42-43)
  • O2 voltage changes (seemingly reacting to the issue)?
  • The timing advance changes (expected, right?)

Based on the above, this is where I’m headed next but really where I’m looking for advice:

• Address the exhaust manifold to pre-cat leak – Since I can’t snug up the bolts anymore, I’m going to replace the pre-cats (just seems worth it since I’d need to pull them anyways)
• MAP – OEM is expensive ($150) so I’ve been holding off
  • Based on the symptoms, should this be replaced?
  • Anything else I can troubleshoot to confirm if it’s good or bad?
  • It’s odd to me that the MAP would fluctuate during the larger stutter/misfire events. Is it a cause or effect?
  • Would the MAP see impacts of something post-combustion (say leaky exhaust causing the O2 sensors to have false reading which would then adjust the IAC, which would then change the pressure the MAP would read? I wouldn’t think a change in fuel from an O2 sensor reading would impact the MAP, right?
• IAC – Is there any additional troubleshooting I can do? Maybe there’s a bad signal or shorted wire?
• Cam or crank sensor? Any diagnostics that can be done?
• Grounds – I’ve done a cursory inspection but haven’t pulled and cleaned them
• If all else fails above, a step I would take is to send the computer to WranglerFix for diagnostics. I have no other issues so this would surprise me as the issue

I have a Jamboree coming up at the beginning of August so I’m really hoping to get it sorted before then. That being said, it’s drivable so I can likely run it this way if needed. I'm also planning the full cooling system cleanout/rebuild and suspension refresh as I'm sorting this out.

Any help, advice, or other insights are hugely appreciated!

Thanks for the replies I’ll check into both.

@MikeE024, thanks for the screenshots and extra info. Definitely a great point and ruling that out would be a major step. I’ll give them a call tomorrow for a few questions. The diagnostic service looks like a good option. Just will put me without the Jeep for a few weeks but that will only hold up the coolant flush process. I can still work on the suspension, oil pan, and probably the pre cats.