I have an 00 Ultra Classic with similar problem. After starting it will run high then I shut it off and restart, it acts like it wants to die. Seems the idle is too low. I'll try the reset.
On a '00 with Magnetti Marelli injection, make sure the "air bleed" screws are clean ( carb cleaner.) They're located at 1:00 and 11:00 as you're looking down the dual throttle throats ( Look up!)