I have a 2006 Ram 3500 CTD with the automatic, it has right at 103,000 miles on it now. Last week when it was cold here, -5F, I had the block heater plugged in and started it up, it ran real rough for a while, the check engine light was on and it then clear up once it warmed up a little and ran like it normally does. I drove it into town and filled the tank up, before filling it up I did add around 12 OZ of Howes diesel fuel additive, I drove it some more and the check engine light went out. I drove it again yesterday, not since the last time earlier in the week, and it started running real rough again. The check engine light came back on I stopped at a NAPA store and bouht some more fuel additive that is suppose to increase the C tane and clean the injectors, drove it home, 3 miles or so and parked it. I had tried draining some of the fuel out of the fuel filter with the stock drain the first time it started acting up. I took the fuel filter out of it today and suck most of the fuel out of the filter housing, it was full of very small gunk, the filter is black looking and when I drained the remaining fuel into a container it looked like it was full of gunky debris, black dirt looking. I try flushing the fuel filter housing out with some clean deisel fuel and installed a new fuel filter, I filled the fuel filter housing up with clean diesel fuel and cycled the key multiple times to make sure the fuel filter was full, it was leaking I finished tightening up the top to stop the leak,the new O ring had not seated properly , evidently I started it up and let it run, it seems worse now (it was up to 45 F here today ) and I checked the exhaust manifold ports with a infra red temp. sensors and the front two cylinders are not making any heat in the exhaust manifold ports, the other four had between 185 F to 285 F and the front two had 85 F Any suggestions, help or fast fixes will be greatly aprreciated Thanks in advance for the help


UPDATE, 12-27-13 I've been out of town since the 23rd, I started the truck up before I left and it seemed better as far as the idle. It was warmer that day but I did not drive it. I started up again today and drove it, it was above 50 F and it runs fine now The check engine light was on before starting it but it went out after driving into the gas station I bouht the fuel from and starting it several times before I got there. I had several other stops before the gas station so I think it got warmed up and then on the last restart it did its self diagnoses, if they diesels ECM do that, and the light stayed off I did take it to the loal NAPA store to see if they would look at the engine code but they say they don't do that I'll take it to a good shop on Monday and ask them to down load the history and see what the code was or is, I'll post the results from that then Thanks to all of you who chimd in for the help