Well I went to the dealer at AlamoPlex in San Antonio for the rear brake recall ( #2) yesterday and told them about my problem with the vibration ( pulsing) with braking. When I made the appointment, I told them I wanted them to measure run out on the rotors ( front and back) to look for warping. They did the recall, both technician and foreman tested the bike, measured the thickness and checked for warping of the rotors.
Run out on the rotors .007" and thickness is 4.95 mm. Both measurements in spec. They said the ABS kicking in is causing the vibration( pulsing). I have owned this bike since new for the last 4 years and something has changed. I will try cleaning the rotors s suggested by Brian and see what happens. They told me that the cost of checking the rotors would be $94 if there were no abnormalities requiring warranty work, but after all the work they did, the cost was "no charge". Go AlamoPlex...I have always been treated well by these guys despite the fact that I did not buy either of my bikes from them ( Concours and GSXR).