Prior to owning the R3 working on cars the caliper guide pins are usually a little stiff which is still acceptable, on the R3 it's not acceptable to have any real stiffness sliding the caliper on the guide pins for the rear caliper. This was causing the rear disc to get hot and I mean really Fkn hot. After pulling the pads on mine I tried to slide the caliper on the pins - it was a no go. Not until I found the front pin was binding/grabbing or stopping the caliper sliding did I fix the thing. Now the caliper will slide on the pins freely with almost no resistance - I now have a cool rear disc no longer does it get hot from just normal riding. I can grab the caliper and rock it on the pins and I feel the slightest free play or movement (before I cleared the front pin stiffness - it was solid with no free play at all) this was causing the caliper to bind on the pins with the brake applied and it wouldn't retract properly causing the pads to then bind because the caliper was sticking on the pins.
If it's not the issue on your machine then that's good, others however with a similar issue might want to check the caliper pins for freedom of movement before you start looking elsewhere - just remember the caliper should float on the pins with little or no resistance.
Hope this is helpful to someone.