I run a JG Edelbrock plenum inlet on my integra with headers, 2.5 inch zorst. When i had the car stock with that manifold ive never seen a problem like this, infact the car runs better with the manifold, just drinks a lil more juice. Even when i had the 25% larger t body running all with stock ecu didnt have a problem, apart from the fact that the t body was faulty, but that aside it might be wise to check out hose connections ect, make sure there is no vac leak and make sure everything like idle bypass motor is all tight as that does funny things when not secured to the plenum properly (read: i left some1 else to tighten that and didnt check it) wondered why my idle was over the place.