If your RPM's are wandering at speed it shouldn't be the ISC unless it is broken. And no, it shouldn't be making noise after bike is warm. Was it replaced??
Are you sure the noise is the ISC and not the secondary stepper?
Maybe replace the throttle cable or at least lube and adjust to spec.
A short somewhere could cause ECM wackiness.
Is it repeatable or totally random?
I know you said you cleaned the throttle control area but I had a big beetle get wedged in there once and RPM's went from 900 to 1200 to 2000 over an hour.
I'm no mechanic but I did unhook my Primary Stepper Motor and tucked it into the area where the plenum was and into the rubber oval leading into the battery box but not inside my nice toolbox/glove/snack box. PS. My water bottle is under left side cover.
NOTE:
IF you do decide to remove it make sure to also take out some other parts of the assembly to avoid
what happened to me. See pictures below.
I set the idle manually and everything was fine and took it for a ride. I hit a bump 50 meters down my street and the piece that rotates flipped
around and caused the bike to go to 100% throttle. I had pulled in the clutch just as it happened so no wheelie and I hit the kill switch immediately. Scary and loud!
I had to push it home and removed the other bits and have never had any issues since.
If cold, I just hold the throttle until its warm or set the manual cruise control to 1,000 RPM for a minute.
"Primary Throttle Stepper Motor = ISC
Stepper motor used to vary throttle opening at idle and when the engine is cold."
"Second throttle stepper motor - situated between the throttle bodies for numbers one
and two cylinders. In response to direction from the ECM, the second throttle stepper motor moves the second throttle spindle to the
position directed by the ECM. The second butterfly epitomises engine torque by maintaining intake air flow speed.
It does not act as a choke for cold start purposes."
I haven't heard of issues with that one and the secondary butterflies wouldn't cause high idle - especially if you set them to 100% open in the tune.