Here are some things that come to mind:
Please clean your injectors with Lubro Moly Diesel Purge.
http://www.youtube.com/watch?v=-3zpwPNijnI shows how it is done on a VW TDI. You run the cleaner directly into your fuel line connected to your fuel filter into your engine so you have pure cleaner not diluted by the diesel. I've done this with great results in my TDIs and so have many other diesel owners.. If you can't get the Lubro Moly Diesel Purge, do the same cleaning using a mixture of 50% diesel blended with 50% biodiesel. Here is another example of how it is done on a VW TDI to help you do the same on our CRD (one line to fuel intake and one line to return line going back into bottle)...if you do have a lift pump, disconnect it electronically.
http://www.tdiblog.com/tdi-do-it-yourse ... sel-purge/ You can get a pro version of diesel purge from:
http://www.idparts.com/catalog/product_ ... ts_id=1971You could have gotten a bad batch of fuel. If you do the diesel purge you are burning only it and no diesel from your tank and if engine runs better, you got a bad fuel or fuel delivery problem. Every once in a rare while, a fuel delivery truck accidentally pumps gasoline into the diesel tank. How poorly, if at all, it runs is determined by the gas/diesel mixture percentage.
Could the bad idle be caused by a stuck airflow control valve? It acts as a throttle to close intake to force more egr gasses into the intake. I had one fail and I'm almost sure I had the same error code you had thinking it was the EGR when in fact it was the AFCV (not 100% sure hopefully somebody else can chime in here)
DO YOU HAVE A LIFT PUMP or new FUEL HEAD? Air in system can cause a bad idle and cause engine to run very rough (ask me how I know). I'd spend the couple hundred bucks for a new fuel head (a racor is awesome and I change the fuel filter every 50k miles) and a small external lift pump is fairly easy to install. Consider running some clear fuel line from your fuel filter to the fuel inlet line and see if you have air in your fuel. If so, that's probably your problem.
Consider unplugging your battery overnight and turn your headlight switch on to discharge any stored energy in any electronic's capacitors. Next day reinstall connector and see if start improves.
Stupid question for you. How did they determine the cylinder had low compression? Did they do a compression test or was that their educated guess? I am not impressed with dealers and mechanics in general and can you be sure that the cylinder damage (if it exists) wasn't caused by the dealership breaking a glow plug tip when they pulled it out to do the compression test and not taking credit for it.
Did they reuse the glow plug? I would never reinstall a used glow plug when pulling one out for compression test. If they did a compression test, ask to see the recorded value. Did they ensure that the glow plug had no damage on the tip...meaning no part of the tip had broken off and fallen into the engine?
I don't know if its possible but consider switching injectors temporarily and see if the noise comes from another part of the engine.