I don't have my car out front, but there should be a throttle stop screw somewhere. With a different intake manifold, you are changing the breathing characteristics of the engine. The IAC should adapt for this, but perhaps the computer is confused with the new intake, and it has taken a while for the computer to adapt. Try disconnecting the battery for 5 minutes, reconnect, restart, and see if that fixes it.
If it comes back right away, or after a few hundred miles, try adjusting that throttle stop screw. Also check the TPS as another suggested. Other possibilities include the Air Charge Temp sensor and Coolant Temp Sensor (make sure to get the one that goes to the PCM, not the instrument cluster).
