My 2003 Cummins seems to have a knock and I can't figure out whats wrong with it.  First of all here's what it has for mods, fuel related: Bully dog triple dog with 2.3.4 download and Industrial Injection 90 HP injectors.  When the old ones blew it filled the case with diesel but I didn't run it anywhere and no damage to motor was apparent.  after the new injectors were put in it only seemed to knock when I accelerated quickly.  Now it seems to have a constant knock and as of today there is a "pulsing" noise in the exhaust, worse in the cold too.  Just a really loud rough running motor, for a Common Rail.  The knocking seems to come from the bottem end of the engine but that's just from my ear.

I have no pump upgrades and no bad fuel in the system.  My EGT's, engine temp, Oil pressure all seem to be normal.  Still blows black smoke and no fuel is found in the case.  Everything is working fine but I can feel and hear it pulse while driving and idling.  Some tell me it's just the CP3 pump trying to keep up and that a high flow lift pump would quiet it down. (such as fass fuel or airdog)  I do have the Airdog High flow lift pump and air seperator but I have not installed it yet.  I could really use some help/advice.  I have to drive the truck from Minnesota to Texas in 3 weeks!  

Try having an overhead run I had mine donr last week based on the advice of a friend who used to work on the cummins in big trucks. Mine had a knock in the top end he said that the valves needed adjusting. They reset them at my local dealership, said they were out of adjustment a little seems to have taken the knocking out.  

I just caught that your problem seemed to br in the bottom end I guess my advice is useless. sorry.  

Hate to break it to ya but you probably had your oil diluted with fuel when you had your old injectors in... after that damage is done.. How loud is the knock? you could always pull the pan down and check out your rod and main bearings .you can pull all the bearings out if you just roll them in. Its really easy. let me know if you have any questions.  

the knock isnt very loud it's like a dull knock.  Most people can't tell it's even knocking but I can hear the truck doesnt sound right it its running rough anf chatters more than other CR's.  Sounds kind of like a older 24 valve.  I'm not sure if it makes a difference but the old inejctors blew alomost a year ago now and I've driving it over 2000 miles since.  

It may...but did the noise start right after you put the injectors in? The fuel pump and injectors are calibrated into the computer with a certain trim code and if they do not match they will make the engine have a slight knock...if that's the case then it shouldn't hurt anything....it's just something cummins did to reduce noise in the CR's.  

It knocked alittle before the injectors but only when I would accelerate quickly.  Today I upgraded the knock to a clatter, it's getting worse.  I can feel the vibration in the steering wheel and pedal now. I think I'm gunna take it to a shop this weekend.