Take the side cover off the injection pump housing. Inside you will see the rack bar that the governor moves back and forth, twisting the pump plungers to control the fuel delivery rate. The pump plungers have a gear quadrant attached to the bottom that meshes with teeth on the rack. There is a dot on a tooth the rack for each pump plunger and a dot on each plunger gear quadrant that must point to each other. It sounds like one may have been installed "out of time".
The advice about checking the pump lifter heights is good and will set the timing back to spec even on an old engine. The pumps are removed from the injection pump housing to check the lifter height with a depth mic. When they are replaced, the dots are matched as the plunger is meshed up with the rack.
The picture shows injection pump housings from a 6 cylinder engine but it uses similar lifters, rack, pumps, governor etc. One thing that may look odd is the picture with most of the pumps still installed is shot from the "engine" side after the housing was removed from the engine. The other one with the depth mic is the way it looks installed on the engine. No need to remove the housing from the engine unless you are getting fuel in the oil! You can see the rack running across the top of the opening and the adjustable pump lifters below it. I cannot remember if the dots are visible from top or bottom, I am thinking bottom, so get a good light and look up at the bottom of the rack and plungers to check for a mistimed pump.

D2-5J's, D6-9U's, D318 and D333 power units, 12E-99E grader, 922B & 944A wheel loaders, D330C generator set, DW20 water tanker and a bunch of Jersey cows to take care of in my spare time😄