That sound better mate...have you checked run-out on your drive flanges/hubs? As in my experiance this is probably what is causing the run-out in the discs in the first place.

Also don't forget that there is a chance that the disc run-out 'spots' [where the disc has been touching the pads] could have been work hardened [due to the elevated temperatures provided by the friction at the pad/disc contact] and therefore when you put the discs back on the vibration may re surface due to the work hardened areas not wearing as fast and again producing varying disc thickness and hence run-out