when I first got my GTR it had a "mines" ECU. I had it checked out and it was a faulty standard ECU with a mines sticker on the side. It was causing the engine to run too rich and causing the spark plugs to foul up. This would characterise itself in the form of the engine cutting out, small to medium size plooms of black/brown smoke (unburnt fuel) out the exhaust and on ocassion complete stalls. Unbeknown to me I tried to have the standard ECU remapped but it was at this point after hours on the dyno I found out from another mechanic that the ECU was actually faulty and causing all sorts of missfire issues. Problem solved when I had the PFC fitted and tuned the AFM's were fine.
not saying it's definately the ECU but if after you swap over both AFM's you are getting the same/similar problems you might need to look at the ECU after say spark plugs, and check coil packs etc.
Cheers
PS: R31nismoid did you get my pm?