I took off my JoeP FCD when I installed my EMS. The EMS helps with cut, so no more need for it. If your MPI uses the MAF signal then try taking the FCD off, as it might be pulsating your MAF signal or something. Just cut the FCD wire for now and see how it runs. If it still happens then just reconnect the wire.
BTW welcome to the forums, haven't seen you around but it sounds like you are on the right track! Kick ass man.
BTW welcome to the forums, haven't seen you around but it sounds like you are on the right track! Kick ass man.