My old Kubota did the same thing last spring. Took me forever to figure out it was just one injector acting up. That hiccup sound is so annoying to track down.
My buddy's F-250 had a similar stutter that turned out to be bad diesel. We spent a whole Saturday convinced it was the fuel filter before figuring it out, lol. Diesel engines just have a special way of keeping you guessing.
Sounds like diesel injectors have a talent for turning a simple fix into a full day project. @vale19's Saturday fuel filter adventure is proof they enjoy the game as much as we hate it.