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Hope you don't mind me asking Mike, but for the sake of learning, how would that happen? It's my understanding that to shut down a diesel, you have to remove fuel, so in this case, the fuel is still being injected into the cyl's. Would a shorted glow plug relay back feed current to whatever shuts off the fuel?
It should be near impossible for a run-on with these rigs: The Injector Driver Module must fire the injector or there is no show... no matter what the fuel pump is doing. Starving the injectors of fuel on a HEUI system is not just bad form, it can damage the injectors... your dad's suggestion is for "legacy" diesels. There is an issue with the ignition system allowing the IDM to continue firing, it needs to be resolved.
I'm still thinking ignition switch. It would have to still have power to the IDM and PCM relay to keep running. Something could be back feeding them or one could be feeding the other, but the ignition seems most likely. There is more than one circuit in the switch, so some things could shut off and not others. Both these relays appear to be on the same circuit in the ignition switch.