The idle will settle down, so long as The Groove is in the correct position.
When you first start the engine post-mod, just don't touch the gas pedal. This gives the computer time to start making its adjustments without passing the Groove, which can throw the ECU into conniption fits!
Do quite a few restarts, not touching the pedal until you're ready for the test drive. 9 times out of ten, any issue the ECU may have had is gone by the time you get to the drive.
The exception is if you've cut too close to the plate on computer controlled throttles. If they race to 2500 rpm or more, then idle down, The Groove is too close.
Hope this helps!