Troubleshooting a rough running engine in a TJ

get_me_outta_Indiana

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Original poster
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Apr 13, 2020
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Location
Montana, USA
Long time lurker turned poster by an unprovoked rough start this morning in my '06 Wrangler (2.4L, manual transmission), currently approaching 68k miles, no major deviations from stock machine.

The problem
Started the car this morning after sitting for ~36 hours, startup was "rough". Vehicle shook somewhat as engine lurched through ignition. Idle was also "rough", more low-end noise than typical with accompanied dissonance akin to a subtle grind. I turn the vehicle off and checked oil levels — all good there. After warming the car up, I drove the errand (~5 miles) as intended and made these notes:

1.) Problem showed minor/negligible improvement as engine approached operating temperature
2.) Engine makes similar whines as it does when in 4WD-Low when approaching RPMs in excess of 2k RPM (2k RPM is cruising speed for this vehicle).
3.) Engine sounds "rough" both when accelerating and particularly when accelerator is relaxed and the vehicle begins slowing/engine braking.
4.) Engine sounds "rough" as in #3 even when revving while in neutral/not moving.

Pertinent recent history (provide context, may or may not be relevant)

1.) The weather has been reasonably chilly (between 15'F/-9C and 32F/0C) during the past 36 hours, car was stored outside.
2.) Vehicle was driven through snow 36 hours prior; 4WD-High was used. Noticed some trouble getting 4WD-High to engage after hitting some wet slush at moderate (30 - 35 mph) speeds, but tried again a mile later and difficulty disappeared.
3.) Serpentine belt was replaced four days ago due to old one showing modest cracking due to age.
4.) Oil was changed with manufacturer recommended weight four days ago within interval.
5.) Battery was removed at time of serp/oil service to allow for dry cleaning/dirt removal as I was enjoying the sunshine.
6.) I found a moderate crack in the exhaust manifold during October 2019, ~3,500 miles ago and patched the cracks with JB Weld. I have not inspected the crack since, but this issue presents differently than that issue did.
7.) TPS was replaced due to original TPS failure during March 2019, ~ 7,000 miles ago.
8.) Spark plugs replaced March 2019, ~7,000 miles ago.

Any thoughts about where to begin troubleshooting the engine "roughness"? My suspicions are currently focused upon the transmission, prompted by Recent History #2, although Observation #4 seems to rule this out. Where should I begin?
 
Try driving it for a few hundred miles. You removed the battery prior to this happening and it takes time for the engine control computer to readjust. The computer self adjusts based on many factors and needs to “relearn” your engine’s specifics.

Good luck!
 
The noise you describe as similar to 4LO whine sounds allot like an accessory drive issue. It might be related to the belt you just replaced. The new belt or replacing it might have pushed one of the bearings over the edge. The alternator, idler and tensioner, the A/C or the power steering. The extra load may be causing the engine to struggle a bit more than usual at idle. The engine sounding rough and difficulty getting in 4HI might suggest a motor mount is damaged. Those are areas I might look into.