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Sometimes at idle the engine gets this muffled sound, no pleasant diesel knock, and runs rough. When that happens I get diesel exhaust in the cab as if the exhaust is pumped directly in. It has little power for a second or two on acceleration, until the knocking comes back.
I think it is related to the turbo back exhaust or EGT sending unit (in the driver's side manifold) I installed even though it has only recently developed.
I think that the exhaust coming from somewhere before the turbo. Had that muffled sound, when I put my turbo back in, and it turned out the up pipe was off centered, so it was blowing smoke big time at the clamp.
Your problem probably because of the rough idle, and the whole engine's "dancing", that's why the exh. gas finds the way out. Find the cause of the rough idle, that sounds more important to me, than the exh. gas.
If my understanding is correct, the motor will get quiet (or quieter) at idle when the EGR sticks open. It could also explain the rough running and lack of initial power. Can't explain the diesel exhaust in cab smell as it relates to your problem.
If you're running with the EGR unplugged, then I'm probably wrong. If you're running with it plugged in, then I'd pull and clean it. Can't hurt.