Time for an update I think - so far the list of components I've replaced on this vehicle is up to:
PCM Powertrain Control Module - this thing runs the engine basically. It had a damaged 5vDC output regulator - this runs the sensors on the engine etc.
BCM Body Control Module - main ECU basically. The vehicle has two networks, high speed and low speed and this is the only place the two networks intersect.
IGCM Instrument Gauge Cluster Module - this has a CANBus hub in the back of it and that hub wasn't talking basically. This is likely the cause of the generic fault codes and limp mode issues
Fuel Pressure Regulator or SCV - electrically damaged
Throttle Body - throttle flap position motor electrically damaged
Fuel rail pressure regulator - pulled to check due to performance questions, found that Ford factory had literally dipped the end of it in thread sealant. The hole in the sender was blocked with crystallized thread sealant and the bottom half of the common rail was full of thick white jelly which looked to be diesel hydrolised thread sealant. Thanks Ford...
Two injectors, one electrically buggered and the other partially blocked (got a set of five in it - testing the injectors and fitting replacements has been the most expensive part of the work so far)
Also bypassed and deleted the EGR as part of this set of works.
Seems to have cured the issue - waiting on a compact split-style hall effect current sensor to do a final check on a couple of components and this style of sensor doesn't seem to be available in NZ that I could see. This will confirm if there are any other issues with a couple of the engine management components.
With the fuel consumption of this vehicle vs the equivalent new replacement in the same useage - it looks like the repair cost will be recouped in less than 50,000Km's just in the lower amount of fuel burned vs the newer auto-transmission vehicles. Worthwhile doing I think, but it does show the very real limitations in relying on on-board OBDII diagnostics on these vehicles. When the issue is in the CANBus communications network and computer side, modern parts-swapper 'mechanics' seem to be completely out of their depth. It has taken a long time to gather the evidence to support the theory that this was not a mechanical issue in the fuel injection system.
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