I知 not suggesting this is the cause of your low RPM knock, but I have seen this happen more than once. A crack shaft will break just forward/behind a main journal and continue to run without causing any apparent issues other than a low RPM knock.
The first time I seen this happen, I wrote it off as an odd occurrence mainly because I had never seen or heard of it happening before and it seems impossible. I have seen it happen twice more since then. At a idle, you could hear a hard knock in the engine(sounds like a rod), but above 1,200 RPM the knock goes away and the engine runs smooth. No knock or vibration.
All of these were large tractors (over 130 hp) and I have never seen it happen on a 3000, but I would say its possible. Obviously, this isn稚 a good thing and I can稚 say why or for how long a engine will run, but I do know that one of the tractors was ran for over a half a day (under heavy load) after the knock was heard before I stop it.
I do agree with a possible fuel system problem.