Did the shaking occur before or after the brake job? What rotors are they? What was wrong with the originals? I heard you cant or not supposed to turn the originals, not sure but if you can then do that. Stay with original stuff especially on a BMW. I wouldn't use a wire brush on the rotors anytime!! The pad is suppesed to make itself bed into the rotor and scoring from a wire brush won't help any! Did all of your pistons in the calipers retract nicely? Just re-trace your steps you might find the problem.