Ok, this might be a long shot, and I will point Kev to this thread to shed some possible light, but I have a suspicion that if you have carried out all those steps and the bike it's still not idleing then the culprit may well be the TPS (Throttle Position Sensor) which it might either need adjusting or, if your bike its a 2005-2006 it may well be that it might have skipped the TPS recall that Yamaha issued at the time, replacing them all free of charge to all owners.

Now Kev will ask you to remove the TPS and read him the serial number once hew knows that he will tell you if your TPS falls under the recall range or not and he might have to give you further suggestions.

good luck and don't worry one way or another we'll get to the bottom of this.