+1 on the warped disc.
I suspect its warping as the pads are
dragging due to old caliper seals hardening up and not releasing the piston.
Have you ever changed the seals out?
Yamaha recommends changing them EVERY TWO YEARS. I'm still on my original rear seals but the fronts were rebuilt at roughly 12,000 miles due to dragging..
Its a pretty easy procedure, especially the rear. Its a lot cheaper than replacing new pads/rotors often. Your mileage should go up too especially if that rotor is getting that hot when the brakes are NOT applied... That rotor should stay cool when not applied.
Even with a slightly warped rotor, new seals will allow the pads to retract as they should. You'll still have pulsating in the pedal but the rotor won't be hot and you won't be prematurly eating up your pads.
BTW, when I rebuilt the fronts, I felt/compared the new seals to the old seals,
I could not tell ANY DIFFERENCE. Age/heat take a toll on the rubber seals, the seals will stick and not release the piston. The front wheel, when lifted off the ground (centerstand and sizzor jack under the header) now "free spins" by hand,
4.5 full turns vs before the rebuild, about
3/4 a turn... That was with about 5 years on the original seals, not two years...
IMO, new rotors/pads without fixing the real problem will have you chasing your tail and throwing your money away....
You also want to pull the two
caliper mounting bolts. The caliper and two bolts tend to gum up if not serviced and will not allow the caliper to move when the pads wear with time. Clean the bolts, the holes they go into and re-grease (Use brake grease due to the heat and it won't fling out/drip). They make brake specific grease: ([ame="http://www.amazon.com/Permatex-24110-Caliper-Brush-Top-Bottle/dp/B000HBNV6W"]Permatex 24110 Ultra Disc Brake Caliper Lube, 8 oz. : Amazon.com : Automotive[/ame] ). They should move very freely. I just ahd to replace a rear tire and had previously cleaned and lubed those bolts/pin's. They were starting to get sticky and got serviced again. They now move nice and freely allowing the caliper to move as it should...
The rear seal kit, at least in the US is about $6.00 USD,
http://www.partzilla.com/parts/sear...4/FZ6+-+FZ600SS/REAR+BRAKE+CALIPER/parts.html