I am hoping someone can give me a couple ideas before I have to take it to the shop and let them diagnose the problem.
Kind of a long story, so here goes.
04.5 with 119K miles. For a couple months there I had been getting random P2121 codes. I cleaned all the grounds and then finally replaced the original batteries last month. I figure 10 years was a good run, so I had the dealer install two new ones. I haven't had a code since, but I still get a pretty steady miss at idle. Once the RPMs get to about 1500 or so, it smooths out. I tow an 18K lb trailer and under power, I still have plenty of power and the mileage is still good. The miss only occurs when not on the throttle basically. Its not making oil at all. It has had an Air Dog with 3 micron filters for 70K miles now, so I don't see dirty fuel being the problem.
Trying to narrow the problem down, with the truck idling, I sprayed the exhaust manifold with water thinking that the missing cylinder would be cold...except the water evaporated from all the manifold ports at the same time. So it seems that there isn't just one cylinder that is the culprit.
I unplugged the Juice and it has the same miss/vibration.
It doesn't throw any codes at all since the new batteries, but there is a definitely a stumble when taking off from a stop when unloaded.
Is it possible that the rail pressure is low and causing it to just run rough until RPMS come up? Is there anything I can look for?

 

I checked the codes by turning the key on three times and all I get is P0477 which is the exhaust brake driver (PacBrake PXRB) which works fine.
I went by my local diesel shop I trust and he said it sounds like an injector, which is what I feared. He told me a new Bosch injector is $270, and new crossover tube is $55 (if needed) and labor would be another $90 or so. Sounds pretty fair to me. I just hope its only one bad injector.
I just don't understand that since this thing has a cam and crank sensor, why it can't tell me when, or which injector is missing.

 

It does sound like an injector issue, hard to say. My Rail pressure dropped at idle with 87,000 miles on the truck. Sent the injector off to F1 diesel, 3 flat out failed, one was boarder line bad, and the other two were OK. I had them all redone.

 

You may not be as lucky as me but I bought fuel from Tesoro one time and I had the same problem as you till I fueled up again at my regular station,,,I though I had a bad injector just like you but im sure it was a bad batch of fuel, just something to think about.

 

I've run it about 1500 miles, all on fuel from my normal station with Power Service added.
I'm going to take it in on Monday. I'll report back when I find out what it needs.

 

Shop put the scan tool on it and disabled the injectors one at a time. #6 checked bad and the throttle position sensor P2121 code came back as well. I'm going to have them change the injector and sensor since they can do it cheaper than I seem to be able to get the parts to do it myself.

 

New injector and throttle position sensor and it runs like a champ again. Hopefully it will be another 120k before I have a large repair bill again.