I believe I addressed this particular problem with two replies I wrote earlier. I also have an '09 but think your description of the symptoms and mine are only differentiated by semantics. These are the two replies:
(Quoting maxtog, "Well, I know there are some good uses for it, but I was actually trained to NOT use the rear brake, for safety." Whoever trained you didn't know much and contributed to the "blind leading the blind" axiom. I started riding motorcycles when I was 14 and am still riding at 70. For all of those 56 years it has been both on the street and in the dirt. When I started there were no dirt bikes, you created a dirt bike by modifying a street bike. My first was a '55 BSA Gold Star. I still ride my far more modern thumper in the mountains and one of my street bikes whenever I have someplace to go. I have racked up beau-coup miles and each and every one of them included use of both brakes. I find it amazing that so many of you think that use of the rear brake is a superfluous effort. The mention of using the rear for better control at parking lot speeds is a perfect example of useful rear only use. There are numerous situations where a proper modulation of both brakes makes for a far more pleasant and much safer riding experience. My C14 is an '09 model with ABS. The first time I rode it I realized that the rear brake was just about useless at parking lot speed as it had no feel at the lever. I solved that problem by removing the return spring that attaches to the pedal itself. This spring is not necessary as the return spring in the master cylinder is plenty strong enough to return the pedal to its normal position. With the external spring removed the lever pressure could be discerned with the foot and I then knew how much brake I was applying. I strongly suggest that this unnecessary and potentially dangerous spring be removed so the rider can tell how much pressure he is applying with the foot. Try it, if you disagree you can always put the damn thing back on the bike.)
(Sorry Martin, you're just going to have to get off your lazy ass and go out and look for it. I just got up off mine to go out to my shop to verify my memory of the spring's exact location. In order to take a picture of the spring I would need to put it back on my bike. That is not going to happen because the brake pedal must be removed to remove or replace the spring. It's behind the brake pedal. There are two springs, one is very small and operates the brake light switch and the one in question is much larger and is a brake pedal return spring. Because of it, you have to apply so much pressure with your foot that you cannot tell when the brake is actually being applied to the caliper and rotor. Because of this I damn near tipped the bike over in a parking lot at less than walking speed because I could not properly modulate the pressure being applied to the brake due to the lack of feel. This happened when the bike was less than an hour in my possession and that damn spring was removed within an hour of my arriving home. It's easy to see and not at all difficult to remove or replace. I am living proof that any ass can do it.)
As for the "black pepper" you see. Brake dust does not look at all like black pepper to me. I would ignore that for the moment and get rid of that above described spring and its inducement of problems that magically disappear with its removal. Clean the rear wheel, ride it for awhile with a normal and useful rear brake and then check out the appearance of brake dust. The fact that the bike sat unused for three years should not have had any influence on the behavior of the brake. The two calipers and master cylinder for the front wheel also sat idle for the same length of time but working as they should ought to be some indication that lack of use is not a contributing factor.
