From your description it appears that the new pads have introduced your symptom. I replaced my rotors (1997) after about 70,000 miles. The rough pedal was not because of a warped rotor but because of material transfer from the pads to the rotor surface. The metal in the pads can wind up on the rotor and cause a rough finish. When this happens the pedal pulsates a bit when braking. The cost of a new rotor is not that expensive ($20 or so at Autozone) so it is not a big deal to replace them on occasion.
I recently replaced to rotors on my Mazda tribute after 23,000 miles because they were scored. My wife's driving habits tend to eat up pads on her cars.
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