It could be something within the injector system.
It seems weird but I had a similar issue with an early 740 with C9. Lost power out of the blue. Idled poorly and barely pulled itself running empty, would die when engaging seperator even. Changed fuel filters with little benefit. Talked to a few mechanics...same injection design as older Ford 7.3 diesels. They use engine oil within the injection system to operate. Determined one bad injector can really make for a poor running Cat. For some reason, the machine began to run better IIRC. Changed engine oil as it was at about 400 hours IIRC on good synthetic oil. That seemed to help it even more. I tinkered with it, along with the oil change, and it seemed to heal itself somewhat. As soon as Cat came to hook laptop up and did an injector test, #6 injector IIRC was "questionable". They replaced it under the 5 year/emissions warranty and it has been fine since, now at 1100 engine hours.
Never have liked the HEUI sound when starting cold or idling. These fuel systems seem fairly simple, but have some easily fixed weak points. Check valves and fuel primers seem to be common issues. My point of this post is keeping clean engine oil in helps more than just the lube system within the engine, but also is important for the fuel system.
An infrared thermometer on each exhaust port can tell you something. 1 and 6 should be close to same temp, 2 and 5 warmer, and 3 and 4 the warmest and nearly matching. Infrared thermometers can be great tools for many things. An unusually cool port would point to a bad injector. Can check at startup, after engine is warm, and even during operation if your careful.