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Just put new pads and rotors on my 08 MCS. I put green stuff pads and DBA vented/cross drilled rotors on. I notice that the old pad surface did not extend to the end of the rotor (which causes a small lip to form)... the pad surface on the new pads extend @ 1/4 inch past the rotor edge.
I would check the caliper mounts -- loosen and see if they can be moved in a little. Some over hang is ok and not unusal, but a 1/4" sounds like a lot.