It sounds like this stuttering occurs when the system goes into closed loop and the ECU, MAP, IAT, etc. take over. Just for grins try the below procedure to erase all the ECU memory and start with the original factory settings. Also clean up the 60-pin ECU connector first.
Disconnect the POSITIVE battery Terminal and touch it to ground for 30 seconds. (This is to discharge the PCM capacitors, which maintain the Adaptive Memory).
Reconnect the Battery Cable
Turn Ignition Switch to the “On” position but DO NOT start the engine
Turn Headlight “On”
Turn Headlights “Off”
Turn Ignition Key “Off”
Adaptive memory has nor been flashed, or erased from the PCM.
When you restart the engine it will be running off a set of pre-programmed tables that come with the PCM from the factory.
When you get the engine up to operating temperature the PCM will start to collect data for the “Adaptive Memory”.
The PCM will collect data for Adaptive Memory for the first 50 Warm-up Cycles.