Here's how I do it:
1) warm up bike.
2) take off air box, air filter and bottom plate air filter sits on. check to see if the the throttle plate and the inside of throttle body need cleaning. If so, do it clean it good with some carb cleaner. Also a good time to inspect the throttle body shaft for signs of wear.
3) turn idle screw counter clockwise until it is observed that the tip of the idle adjustment screw is not touching (I use a bright flashlight to see).
4) open close throttle a few times. visually observe that its closed all the way.
5) reset the tps with ECM spy or tunerpro
6) adjust to 5.5% (before adjusting make sure your still connected to the ECM, for some reason my ECMspy always has to be reconnected after I reset the tps)
7) reassemble bike (air filter etc), unhook the computer, start bike and adjust idle if bike requires it (my bike runs like crap until I adjust idle at this point). get bike to idle at about 1000 rpm by looking at the tachometer on the bike (don't worry about being hooked up to a computer or 5.5% anymore ... it doesn't matter, all bikes vary on what number works for them)
8) take the bike out for a spin and get it good and warm, when you get back check the idle again. Don't adjust it above 1050rpm. My bike likes to idle a touch under 1000 rpm.
9) The first time I reset the tps I carried my screwdriver with me to re-adjust idle during the next few days to see what my bike liked best.