Might need some more info... does it smell like it's running rich/lean? Are all the O2 sensors hooked up right? Loose plug or coil wires? If you have good fuel pressure, all the injectors are firing right, and your ignition system is working right, I would look at whatever airflow/pressure sensor you have an the throttle position sensor. I would start by double-checking all the connections on the engine and making sure everything is talking to each other correctly. Then maybe look at the megasquirt settings/parameters to see if anything is wrong.
