What your describing is something affected by DTV(disc thickness variation) and/or runout. The rotors are typically cut with the hub at the factory, on new vehicles, to provide the best overall condition for the car. It is not a problem to cut them as most parts have quite a bit of meat before exceeding tolerances. The best way is a method "on car" as it takes into account the hub on which the rotor is attached to. New pads on fresh cut rotors is best. Make sure you don't have a caliper hanging up. Replacement rotors will never be as good because they were not matched to the hub on your vehicle.