I don't know if you may have zapped something with the scan tool, or not. I guess it is possible.
First thing I would do, however, is to pull the connector off the iat sensor. then I would unplug the orange memory wire by the connector for a few seconds and replug it. then restart the car and see if it runs better. I have never tried that so I am not sure what happens when you unplug the sensor. If you still have another car, swap the sensors.
Normally that sensor does very little, but if it goes bad and shows a low temperature, then the car will get way too much fuel and flood