For what you paid they should have steam cleaned the engine and a full detail inside. There was never a bolt in the intake side unless you put one in to lock down the cam. That should be a small hex head plug w/ a copper washer on it. That hole has direct access to the intake/cam assembly so there will be oil being thrown everywhere - including out the hole where that bolt now is. The heat shield is somewhat important because it will block some heat off the manifold from increasing the temps to the thermostat/coolant lines. That heat shield should have 3 small 10mm bolts that hold it onto the manifold.
Definitely go back to the dealership and ask wtf happened. Make them fix everything - and more importantly - don't pay anything else for them to fix it. I'm assuming the mechanic lost the plug and found a bolt that would fit and just put a huge washer on it to get it done. They at least should have told you about it, or offered to fix it later.

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05 Liberty CRD - Sold
07 WK CRD - Family SUV

Well, I've contacted the dealer via email so that I could include pictures of what I'm talking about. I know that he received my past emails. I told him that I want the bolt and heat shield replaced with the correct parts when they complete my recall on the lower control arm. They were out of recall kits the last time I was there for the belt, and they were supposed to call me when the parts came in. I also explained that I'm concerned about the reflash of my ECU even after I made a request in writing that they not do so. Would the new tune switch my glow plugs to 5v, or can the computer detect my old 7v ceramic plugs and leave it alone? I'm not sure how that works. Is there a separate control module for the glow plugs that gets reflashed with the upgraded Chrysler plugs?

I think I'll wait until all of the work is finished before I go see Keith in case they reflash it again, but I'm still not sure why my CEL doesn't come on when I unplug my MAF sensor. Perhaps they didn't reflash it. It does sound different when I plug the MAF back in though. I'm pretty sure I can hear it open up the valve. My oil with less than 400 miles us already black too. With the Eco tune it used to look nice for quite some time.

The Jeep also sounds a little different. It sounds a little rougher, but I think it sounded like that before the tune. IIRC the tune smoothed it out.

If my timing was off, even by one tooth, I would know right? It runs great and the hesitation I was getting on acceleration seems to be gone. I really don't know what could have been causing that in the first place. Perhaps having all the hoses off and cleaned out made a difference. Two weeks ago I also cleaned several cups of dog food and a small rodent nest out of the air box. Perhaps the whole intake system was taking in dirty air with the nest and the cracked airbox hose.

I don't hear any "ticks" or loud "clicks" from the engine, so I don't think that anything is bent in the engine.

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2005 Black KJ Sport CRD,
GDE Full Torque ECO TUNE, GDE Transmission ECO Tune,
Samco British Racing Green Hoses
Build Date 1/05
200k miles.
Original Owner