I think it's important to reverse whatever caused the pipes to turn blue.
Find the cause of the brake disc getting hot, even when not used. Turn the wheel, is there any binding? Brake pedal fee play correct? Brake lever free play correct? Check also while hot. Wheel turns freely when disc hot?
Your bike may be over reving. You should have 4000RPM at 100km/h Maybe your clutch is slipping. I suppose you have the right tyre. Do you have 75mm inner clutch cable length at gearbox? Correct free play at lever, adjusted from push rod? If so, in fifth, foot hard on brake pedal, 2000RPM, let clutch out; the engine should stall.
Do the test only as a last resort.
Dave - the only thing, I could do to reverse this to source some dirty injectors and run them instead of the freshly cleaned ones :)
Rear rotor I replaced today morning before going on a trip of +/- 15 miles. Needless to say, I forgot to test the brake, so a non operational rear brake surprised me a bit down the road, fortunately in a non-catastrophic situation... Anyway, once I pumped it a bit and lightly dragged the rear brake for a while the pads embedded themselves to the new rotor and brake operation is restored to normal. It appears to me, this rotor + pads combo works better, than the old one, as the rotor is not getting too warm after a ride, also it feels like bike is easier to push around. The old one was an ABS rotor, the 'new' a non-ABS one (I have no ABS installed on this bike), it should not make a difference, but it most likely does (however I will report back after a tankful or so, as we all new, how subjective these things are).
4000RPM is 81-82 km/h on the adjusted speedo. Clutch operation is faultless, cable length, free play all set to factory standard. Clutch is not slipping and I have tried your last resort incidentally yesterday, in rush hour traffic I was coasting towards a hard turn in fifth gear, forgot about it and let go of the clutch whilst already maneuvering into the curve at 5-10MPH. Bike stalled, nearly dropping me off, fortunately I managed to squeeze the clutch, saving the bike and my butt :)