From my first hand experience with similar problem, here is what I would recommend doing.
First, inspect the rotors for any dirt and grease - even slightly noticeable. Get a paper towel and clean with alcohol, and avoid touching them with your hands or anything.
Second, make sure your pads did not glaze. Simply pull the pads out, and see if there are any silverish spots on them. In any event, get a sheet of 100 - 200 grit sand paper, put it on the flat surface, and then rub the pad on top of the sand paper with even pressure until the spots are gone and the surface seems uniformed.
Third, there is a chance your rotors are slightly warped, but still within the spec due to the stress. In order to release the stress, and mate the sanded pads with the rotors do the following. Go on the highway at normal highway speed - 60-80 mph. Slightly apply the front brake while keeping the gas on so the pads start dragging. You will notice that as you hold the lever with the same pressure the bike starts slowing down and the lever gets pushed back by itself and you need to apply a bit more gas to maintain the same speed. Do this for about 15 - 30 sec so long as you are comfortable. Then release the brake lever, and don't break for another minute or two so that the rotors/pads cool down naturally. Repeat this procedure the second time, and maybe the third time.
Report back.
Also, get
this dial indicator to measure your rotor runout - you just need to lift the front off the ground - no need to take the wheel off.