Anytime the ECM or the battery is disconnected, the ECM loses power, or the ECM is reprogrammed, the idle quality will generally go to crap. It will learn itself-out after a few miles, maybe as much as 200, or you can spend 10 minutes and get it done right away. Very simple...

Turn off ignition, turn off A/C, apply parking brake and chock wheels, start engine, allow to reach full temp (170+), shift to drive and allow to idle for 5 minutes. Shift to park, allow to idle another 5 minutes. Turn off the engine and wait at least 30 seconds before restarting, but it should be back to normal then

And that's it