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Try cleaning them with brake cleaner w/o taking apart. Mine did same thing and I cleaned and "feathered" the brake while riding in case warped rotor at about the same mileage. It cleared up and I now have 28k miles w/ original front pads.
Do you have a caliper available. Open caliper barely enough to avoid touching rotor. Lift front of bike, spin tire and hold caliper still with rotor in jaws of rotor. If touches either side of rotor...warped... have beverage, replace and ride
I just had my 2008 SG in the dealership for this very problem. They checked both rotors, and found that they both had about .003" runout. HD will only authorize a warranty claim if the rotor has runout of more than .006". The service manager suggested they try a remedy that has worked in the past for them. They have rotated one of the rotors 180 degrees approx. or until the runout of both rotors kind of runs in unison. So far there is a dramatic improvement, although I have only ridden a couple of hundred klm. So far so good. It is a real pain to take the bike in to the dealer as they are 110 klm away.
My Ultra did the same thing. I put dial indicator on rotors and they were out about .012. I installed new pads and it didn't help. Replaced the rotors and check them if indicator and they to were out about .012, but the new rotors stopped the problem. I think the rotors had work hardened and had hard spots in them. Anyway they work like they should now. That does make it hard to stop correctly. Especially if you ride two up a lot.
I posted earlier on this, the reason I say rotors is I had to do a hard stop at a red light because of some one talking on the phone, after I stopped I never let the front brake loose until the light turned green, later that day every time I used the front brake to stop it pulsed bad (lesson learned). Did you happen to have to lay onto the front brakes at any time recently? I have a 00EGC and the rotors ain't cheap, but it fixed my issue, good luck.
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