This symptom is RARELY caused by an electrical problem with the Injection Pump. It can be a mechanical issue inside the pump caused by WVO or Biodiesel damage or even a blown head gasket. First, be sure that there is no air in the fuel supply and no relevant codes by doing the appropriate tests. If a relevant code exists, like a 336 or 1690, replace the crank sensor first to be sure to eliminate it as the cause of the skip. If you have a 251, 253, 1688 or 1689 code these only pertain to the Injection Pump and are strong indications the electronics in the VP44 are BAD, and that the pump is bad. With one or any combination of those codes, and an intermittent miss, I would replace the pump ONLY AFTER DOING THE TESTS BELOW. A 216, 234 or a 237 code CANNOT cause a skip or miss, so they are not relevant to THIS symptom. If you want to prove the skip is caused by an electrical issue THE MOST ACCURATE WAY, hook up an oscilloscope to the ground side of the fuel solenoid and watch the duty cycle, which is the solenoid energized or closed time. The wire you want to find for the scope probe, is the wire closest to the engine in the top pair of wires coming out of the injection pump top cover plate. This is the same wire used to attach performance devices. You MAY have to increase and hold the RPM at the point to where it is missing, to see if the pulse width changes erratically on the scope. If the pattern on the scope looks different on the oscilloscope when the skip is occurring, then look at the APPS signal wire, which is the blue with a black tracer in the APPS plug, with the oscilloscope to see if that signal is inconsistent, or “dirty” when the skip is evident. If it is, that would prove the VP44 is being told to do the skip because of the APPS signal. If the APPS signal is OK then you have to condemn the VP44 computer and replace the pump.
If you don’t have access to an oscilloscope, and the skip is ALSO evident at idle, and you do NOT have air in the fuel supply, do the Hot Wire test above, and if it idles fine, it means the VP44 is being told to skip. Then you need to diagnose the APPS as best as you can with an analog voltmeter as explained in Dead Pedal, looking for needle quiver at the same frequency as the skip. A scan tool or a digital volt meter DOES NOT WORK for this test, because they have too much averaging or buffering in them to indicate the problem dependably. If the skip only occurs at higher RPMs, then you have to hold the throttle at the point where the skip is evident, and then watch the needle for any quivering. If NO quiver, it most likely is not a bad APPS, and if you have codes that could explain the problem, it most likely is a bad Injection Pump.
Another way to narrow down the possible reasons for the miss or skip WHEN THE ENGINE IS SKIPPING, is to loosen each injector line, one at a time, until you find one that makes the RPM or sound of the engine change LESS than another. The less the change, the less that cylinder is contributing, indicating that that is the problem cylinder. If the skip appears to move from one cylinder to another while doing the crack injector test, that is what I call a rolling skip and if it is NOT an electrical issue, like a bad APPS, it means it is most likely a mechanical issue inside the injection pump, like a sticky piston in the rotor from contaminated fuel, and therefore means a bad Injection Pump. This is why you have to do the APPS test to condemn the injection pump. If it is consistently one cylinder, it might be explained by being a lazy delivery valve on the Injection Pump, but I’ve never heard of it in a VP44, and it may be caused by some mechanical problem in the engine. If you think you have a bad injector, which is virtually unheard of with OEM injectors, swap the indicated cylinder’s injector with the one next to it and redo the test. If the problem moves, it is the injector. If it doesn’t move, it is something else.