You could have a bad couple of plugs, a coil pack problem, two bad ignition wires, even the coil or injector drivers in the powertrain control module may be faulty.
Of course, if the engine has low compression or low fuel pressure, it will also cause two to miss, or six. I would test fuel pressure and make sure it is at least 50 or 55 psi then I would see if the plugs are no good. Each coil circuit controls two cylinders so follow the ignition wires back from 2 and 5. I think if valve timing was off, it would cause all the cylinders to run terrible. Test compression to test a engine for its efficiency. Okay did the engine come out of a vehicle of the same year with the same computer?
Friday, July 20th, 2018 AT 3:45 PM