Cat 322CL running rough

Hey guys, I could use some guidance please. Last year I bought a 2003 Cat 312 CL serial CBA01680 for farm use. We had some extra oil and fluid on the engine and it caught a little fire that we put out. Still ran fine but we had to replace the vacuum lines. Right after that a few mins after running it it started running very rough and barely running with a little black smoke. It does not have enough power to do anything and shuts off when you try. We had a mechanic look at it and he thinks it is fuel-related as when he sprays starter fluid it runs stronger. We also had all filters replaced when we first got it last year so those are likely good. We bled the air out of fuel and tested fuel at the top fuel filter and we had good pressure and fuel. However, when we check it at the injector it barely comes out which would explain why it barely runs. not sure if it matters but this happens when you first crank it up and turning up throttle control in cab does not change anything (does not increase rpm or make any difference). We did replace the throttle controller/governor but that did not help. the mechanic now thinks it is after the fuel filter which he says is “fuel distributor” and that is way down bottom of the engine. He thinks we should take it out and have it rebuilt. Any thoughts?