You might as well!
Here is what I used to do:
Drive the car until it's warm.
Dissconnect battery for 15 minutes or so. You can also pull a fuse, but I don't remember what one it is.
After 15 minutes, hook battery back up, and go do a few HARD 3rd/4th gear pulls. In in other words, drive the snot out of it for 20 minutes or so.
This will "adapt" the ECU to your new hardware.