Entire story to date:
The engine was overdue for a timing belt and the CRD suddenly began running rough while left idling for a few minutes. Assumed jumped timing as the culprit.
Spent the money on all the timing tools and the timing belt/water pump kit. When I went to insert the timing pins, they all lined up. Not jumped timing? I did go ahead and replace the timing belt and water pump. Restarted engine to make sure I didn't mess anything up and it ran exactly the same as was expected.
Next was to start diagnosing the problem but with winter approaching and the wife still rolling in the '91 Mazda MX-5 (Miata/MX-5 is a wrecked parts car that we never intended to drive) we decided to take the Jeep to the dealer in October to see if they could diagnose the issue and repair it faster.
They first assumed jumped timing and wanted to confirm all timing marks lined up. Right before they began tearing the front of the engine apart I told them that would do no good since it doesn't have timing marks but uses pins instead. They asked to borrow my tools. Should have taken it home right then.
They confirmed that it was not jumped timing but knowing that I did go through with changing the belt and all, I am sure they thought it had jumped timing and that I just lined it all back up before bringing it to them.
They called corporate for advice and they suggested clean and replace the EGR. After that it still ran the same. They then replace a sensor but I don't know which one since it was not on the bill. After no change, corporate suggested to tear the top end down. They did just that and found a sheared off lifter. The rollers on a few rockers were also collapsed and the cams were worn as if some rockers had been collapsed for a while.
They had changed the oil while waiting for the EGR and didn't know at that time to look for the missing part of the lifter. After replacing the cams, rockers, lifters, EGR, and sensor, 3 months and $3042-USD later, the engine now sounds like what you hear in the video.
https://www.youtube.com/watch?v=2uTSrmS0AhIThe dealer knew we said it was not running properly but said they don't hear anything wrong with it.
We also called corporate and told them it was not running properly after the dealer completed all the work they had suggested. Over a week later the dealer called saying they wanted the Jeep back in their shop to double check the timing. I didn't loan them the tools this time and was expecting them to call and ask for them again. They did not and a week later said they still don't hear anything wrong with it.
Before taking it back to their shop I did buy a recently wrecked 2006 KJ with the 3.7L V6 (nosed into a ditch during a recent snow storm) and figured that if the CRD gets fixed I would just part out the '06 but if the CRD was not able to be repaired cheaply then the '06 would give up it's guts for the '05 CRD and still part out the rest.
I appreciate all the suggestions of what to check next and will do just that as soon as possible.
Just wanted to include all info on the issues with this CRD.
Thanks.