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Thanks everyone for the ideas, the good news is the car is running perfectly on the Power FC now.

Based on the input here I was looking into the ECU power (pin 58) and the ECCS relay for issues. I confirmed that while the standard ECU was in:

ECU pin 58 had no power, and 49/59 and 109 did not have power when the ignition was on (but the ECU was running fine)

The ECCS relay did not click when turning on the ignition, or a few seconds after turning off the ignition

All this points to the fact that there was a power supply problem to the ECU which the Power FC did not tolerate, but the standard ECU did not care about. Incidentally, according to the diagram at EN265 in the workshop manual this means the 02 sensor, VTC and standard boost control solenoid were also not working as they share the ECCS relay's power source. None of these issues resulted in a check engine light

The same diagram EN326 shows that "#8 10A" supplies power to all of these. When cross checking this to the fuse box on the driver's side, the 8th fuse on the left side is "Engine Control 10A". I guess this is where pin 58's power normally comes from but cannot confirm because this car has a modified loom at the fuse box which means that fuse is not wired in any more. Also, there had never been a fuse at #8 and the car had been running fine; weird.

In this case, due to the body loom mods I can't confirm where the standard source was, so we just run a fused 10A supply to the battery. After doing that the PFC ran the car fine, reported the right voltage (12+ v instead of 7.8v) etc. The standard ECU also runs fine, and the ECCS relay is now working correctly.

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