You might want to check the alignment of the caliper. Look at the pads, and see if they are contacting the rotor over the full face of the pad. While most other brake calipers aren't affected by wear or the thickness of the pads, the swinging action of these calipers changes the angle of the pads against the rotor as the pads wear.
The pad on the inside sets the spacing for the caliper: a thicker pad will require the caliper pivot to be spaced inwards from the fork than a thinner one in order for the pads to sit flat on the rotor. One way to check if the caliper bracket needs spacing is to loosen the three mounting bolts and squeezing the brake lever, which allows the caliper to align itself. You can then figure out how thick of washers to use as spacers. It might help to remove the front fender, or at least move the brace out of the way so it doesn't interfere with the top caliper mount.