wire it up looking stock - not every engineer is going to know (or care) that the motor did or didn't come with AFM.
Simon got his TA22 with 3TGTE mod plated with a haltech tucked up behind the glovebox - engineer was more concerned with mounts, brakes, exhaust, etc. He didn't go looking for it and simon didn't make a fuss about it except to say it had been tuned at some shop in springwood.
I think you'll be making a rod for your own back if you try to get an engineer to specifically sign-off on the ECU. Just don't mention the ECU and if asked about it, say it came with the motor when you rebuilt the car (e.g. something vaguely resembling the truth).
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