The Idle speed is controlled via coolant that passes from the Radiator to the Throttle Body then back. As the coolant warms there is a small wax bead inside the idle speed controller that gets soft and changes the idle position. The port on the side of the Radiator where these connect trap deposits from the coolant sometimes and clog up. Especially after the bike has been stored for a long period of time (sat on the Dealers showroom for a year before selling, etc). I would start by checking for a partial blockage there....
The wax bead device you're referring to is the cold start air circuit and should not be used to adjust idle once motor has warmed. (Technically, I believe Yamaha calls it "Plunger Control Unit"). If the coolant ports have become blocked due to solidified coolant, I would expect the engine to run at fast idle all the time as no warm coolant would reach the wax motor.
The idle circuit (as others have correctly referenced with diagrams) regulates air into the throttle bodies via a completely different circuit.