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Last year, I was doing some tuning and using the back brake to lpad down the bike to get some peak load areas of the VE table. The back rotor is blue from the heat. I know, I know...stupid. Anyway, now the back brale groans when I trail coming up to a stop. Is it possible that the heating of the rotor is the culprit or is it the pads? Ive taken the pads off and lightly scuffed them which seems to help, but the groaning returns after a bit. The rotor is not warped.

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I would scrub the heck out of that rotor and install new pads. If rotor is true, then it will be a matter of getting that rotor surface back to serviceable. This is not "by the book", (which says replace that rotor and pads once it has been overheated), but since you are working on your own bike, with a bit of care not to create any uneven areas in the surface, you could probably get away with some 400 grit sandpaper and apply it evenly while the wheel is spinning. Follow up with ScotchBrite and a careful cleaning. Even application will be the challenge if you go that way. This might get a bit more life out of that rotor. Worst case scenario, you have to replace it.
 

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Clean and lightly lube [a little white grease,sparingly used] the area on both ends of the caliper where the pads ride so they can move back and forth freely when the rear brake is applied and released.And you might wanna check both ends of the brake pads too removing any burrs or excessive paint,lightly sanding em to smooth em out,cause that can also cause a problem with them moving back and forth on application.
 

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If the rotor was warped, you'd feel pulsing in the pedal. The likely problem is that excessive heat has caused the pistons in the caliper to hang-up. When you get off the pedal, after using the brake, normally the caliper pistons will retract just enough to clear the disc. But excessive heat can damage the piston seals and dust covers. It can also overheat and damage the brake fluid enough so it should be changed. Sometimes the piston seals just become stuck to the pistons.
Open the rear brake fluid reservoir and remove at least half of the fluid. Remove the rear caliper and, using some sort of flat tool(s) (broad blade screwdrivers will do) pry the pads apart so that the caliper pistons are fully seated into their bores. If the piston seals aren't burned, that MAY free-up the pistons to move normally again. If it takes a lot of force to depress the pistons into their bores, it may be necessary to remove and rebuild the caliper with new seals.
 

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What my very short span of experience in this business has taught me since the introduction of disc brakes is,when the pads are changed,no one seems to know what they're doing or are just plain lazy.Anyways,when the pads are changed, two things should be done to prevent the condition mentioned above: #1-the brake caliper ,where the pads ride,should be cleaned,blown out with air or atleast wiped off so they are clean,and THEN,lightly lubed with white grease or never seize on their contact points in the caliper so they can easily slide back and forth on apllication without hanging up,[which is what I believe is happening in the above mentioned problem] ,and #2-the bleeder valve on the caliper should be opened BEFORE the piston are pushed back in to make room for the new pads,then the master cylinder topped off,but NOT over filled cause there needs to be room for expansion as the fluid heats up.Hope this helps ya out!! Dumber then a door knob,Dave!!!
 

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Rotate the rear wheel while its off the ground. You should be able to feel excessive drag and also hear and see the "high spots" as they near the brake pads looking from the rear.
 
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