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Q: Stumbles once warm on 2002 Ford F-350 Super Duty

Replaced the pressure regulator truck picked up and smoothed out went to test drive it once i got to operating temp it stumbled back to the seemingly missing stage. I am completely stumped as to why this would injector harness's and pressure regulator new fuel filter all connections are tight. if ya have any insight let me know
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Two things I can think of , to inspect , would be the coolant temp sensor and the turbo & controls to turbo. Are there any more specific conditions or description of conditions you can give?
it has been a wierd trip. ok it started by acting like it dropped a cylinder. no smoke no fluid loss no fuel in the oil so i changed the harness inside the valvecover. this did not correct the issue. i replaced the fuel filter and put premium diesel fuel in it still no change finaly i replaced the injection pressure regulator it started up great went for a test drive once the truck reached opperating temp it fell on its face and started missing again. It is still doing the missing when cold even now. the high pressure oil pump is 1 year old replaced it due to a severe oil leak from the old one and it had 156k on it so replacement was better than resealing. It just seems like it is running on 6 cylinders i can drive it down the road zero power but will run. i have checked all other wiring and connectors they seem to be tight and no dirt in the connections i bought electrical cleaner and cleaned them all.
Turbo is fine spins freely no freeplay on the shaft. Im thinking there is some broken or cracked wire im missing that is arcing out. just acts like one or two cylinders are dead. rough idle lacking power. i take that back it feels like it is starving for fuel. before any of this happend once in a while when cold it would turn the mil on and run rough once warm the mil would shut off and truck would be fine now its constant.
not one single code. which points in the direction of mechanical not electrical. I hate to take it to the ford dealership and it be something simple im over looking. Even when it started rough in the mornings and the mil would come on there were no codes present with my otc scanner. I cant find any recalls on it other than the cam sensor which ford replaced under the recall. did injector buzz test all 8 were fine. unless the new high pressure pump is bad i dont understand what else would cause it. I have never run across this problem that couldnt be fixed by what i have already done. Im at my wits end with it.
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