Pull the negative on the battery terminal for 30 minutes or so. Then start the car (do not touch the throttle!!)- let it run for about 10 mins. Turn the car off. Restart it, and take it for a test drive. A better way is to pull the fuse for the ECU, but I honestly don't know which one it is. There is a diagram on the cover of the fuse box, but it doesn't tell you very much. I considered doing this when I put my intake on- but I ended up never having any problems. It smoothed right out after a test drive, and I never got a check engine or anything. A little research (maybe even the manual) should help you find the right fuse. That way you don't lose your radio settings or anything.
Good luck,