I had this exact problem. Put in some Nismo 615ccs from my parts car and put in the ASHSpec ecu set up for them, was running jim wolf on stock injectors. Idle was really rough and it would fluctuate from 1500 down to 200 and I couldn't run above 3k rpms. The problem was that my jim wolf ecu was a single intake, and my ASHSpec ecu is a dual intake. Why it messed up is because I didn't change the setting on my SELIN translator for it to read with a dual intake. Changed the setting and she runs perfect. Weird thing is when I put the jim wolf ecu back in it still ran weird. Not sure what your intake set up is, but from what you said I would say it's one, or both, of your MAF sensors. Very well could be the ecu.