Tim after replacing rotors I attach a dial gauge indicator to where the calipers mount, and check for run out. If any run out is detected it can be corrected with a 10" piece of broom handle and a nylon hammer. Hit on the inner portion of the rotor, not the disc to correct any run out. It is also important to use a tension wrench when installing and tension up in increments. I have used new EBC discs that had run out from new. As mentioned previously really give them a good clean.
Regards Martin.