I had the same problem on my em7-300. It was right around 1200 Rpm. Foot lightly on throttle. Would miss or sort of “gallop” I kind of describe it. Almost felt like it had way to light of a return spring in the throttle, but that wasn’t the problem. Eventually over time it got worse and did it in a broader rpm range. And even got to the point of doing it under load some when I let it get real bad. I changed the pump for a reman because the diesel shop thought it was in the governor. Swapping the pump cured it.
can’t say if you have the same problem as me but sure sounds it. Would only do it when for instance I would coast down into a 35mph zone without downshifting, and then just give it slight throttle to keep it moving through the zone at about 1200rpm or so. Didn’t do it on the coast down, or when I gave it real throttle to speed up. Just that light pedal push at that rpm.