How hard are you applying brake pedal pressure? Are you pushing it to the floor with each stop? If so the ABS will be activated. After installing the new parts, was the system bled? As timmy mentions about the bushings, this may also cause some pedal feedback pulsations. This happens with rotor runout but when the bushings are well worn, it feels amplified.
Check also that the lugs are properly torqued. Nothing like finding one is at 120ftlbs and the others are in the 60's. Especially bad when bedding new pads in.