If that ECU is still setup for a B16, you're probably getting knock sensor faults, and VTEC faults (unless the program was specifically made for that engine and has that stuff disabled). Try the correct ECU for that engine, and then see where you are. You're trying to work on too many variables at once right now; get as simple of a setup as you can, and if that works fine then start adding variables back in until you find which one is causing it. Then you can fix it. You're taking a shotgun approach right now it sounds..