You will likely need to do some basic troubleshooting, much of which can be done through the onboard diagnostics. The ECM is smart and stupid at the same time. It doesn't know if it is receiving bad information unless it is far out of range or missing altogether. Start by going through diagnostics and see if there are stored or pending codes. Read the various sensors in real time by scrolling through them while the engine is running, throttle position, MAF reading, engine and intake air temperature etc.. Since the ignition modules have been changed back and forth, check the plug on the ICM for bent or pushed back pins, possible double gaskets on the plug and make sure it is clean and tight. Push on the plug ends when installing rather than relying on the bolt to pull it in. Check the plug wires for correct routing and integrity, the two different styles have somewhat different connection patterns.