I've had tons of problems with my bike idling crappy. Surging up and down, stalling, etc. The TPS, CO, Fuel trim, TB sync, etc was all done and I still had the issue. So I decided to take off the stepper motor, since it's obviously the devil. Now, I have a DP Race ECU, so my results my be different from yours if you're all stock.
1. Get the bike up to temp fully
2. Go buy some vacuum plug caps in assorted sizes, autoparts stores all carry them
3. Disconnect the plug from the stepper motor, and remove the lines and cap off the plugs that they went to
4. Back out the air bleeds equally until the bike idles good by itself. 1/4 turn at a time. I had to back them out 1 1/4 turns
5. Go on eBay and buy a 748/996 throttle housing with the high idle button
6. Install the half of the housing, it swaps with the stock one
7. Adjust the cables slack so that the button works right
8. Enjoy!
My bike only requires you to have the fast idle on for about a minute, then I roll the throttle forward and is disengages it and idles fine. Here's a video