If you've established that your discs are true, then that only really leaves the "surface conditioning". The amount of friction between pad and disc can be effected by contaminants, such as resins in the pad itself and invisible corrosion on the stainless steel discs. (which contain iron.)
Nature being what it is, these contaminants/corrosions don't distribute themselves evenly round the discs and so you often feel the different areas of friction quite vividly in the form of pulsing or nodding dog syndrome.
Nice clean discs and pads, plus lots of heat and friction will often resolve this and condition the discs back to full smooth effect.
Follow Luddite's link to my instructions as to how to do this. Note this is free!
http://www.ukmonster.co.uk/monster/s...35&postcount=3