Warped discs = pedal travel = Warped discs, as the disc will be pushing the pads out into the calipers more then the piston seals ordinarily would. Only solution is new/skimmed discs to return them to true again.
I have to say though, my car had the 47i6 upgrade before I bought it. The brakes don't squeak and are phenomenal even at 140mph+, to the point where I can trigger the hazards to come on when braking hard. So it is possible to get them working properly.
(obviously I realise I've jinxed it now, and will be joining the complaints line next week)