I dont know if this will help at all, but on my E39 M5, the front thrust arm bushings were a big issue. I had a stoptech bbk with vibration, tried all different pads, race pads to clean the rotors, re-bed according to stoptechs site, etc... Even changed the rotors to brand new oem rotors, still there.
The day I pick up the car after its already sold and am driving to deliver it to the new owner, the car drives amazing! The bushings were the culprit the whole time. Big, well known issue with the E39.
I wonder if it could have anything to do with them on your M3. Good luck, I know how incredibly annoying having brake vibrations is.