It could just be a bad tank of gas. Also you might have a problem with an o2 sensor. Start small though and change your spark plugs first.. i know a guy that had this same idling problem (on the same bike) and was solved by changing the plugs. The problem got so bad that the bike wouldnt even start after a while. It could be something completely different, but it's best to put aside the small stuff first before really tearing it open.

Did you have the bike stored away at all for any extended period of time?

--brandon