Hugh pictures would help alot. Checking for a leak is too obvious, but sometimes well worth it. A twice over the vacuum hoses would be advisable. I would check the AFM. IIRC, didnt you have to relocate the battery and plumb back the factory bov in another area for installation of the FFP? Check that. Unlikely factory ecu IMO.
Duncan's car was a bit different because he ran a manual. Not much chance of eratic idle, hunting or stalling -but autos always. Have you done the constant voltage mod. Do you run a SAFC or SITC with the manual boost controller? Dunno about getn into fuel cut as a scenario atm. TPS, standard rail, old fuel pump and dirty fuel filter, cleaned AAC valve lately -the list goes on mate? Is it running rich, might be dumping fuel. Just want to get down to the simple things.
Is this your sons 25G? Pity if it is. This is why im going manual to avoid a few S1 auto issues. Time for a GTST box in the RWD G??