Sounds like you may have a sticky piston causing uneven wear. Remove the wheel and brake pads, and squeeze the lever while watching the pistons in the caliper. Both should move evenly, so you'll soon notice which one isn't moving. Use a small (9 or 10mm) open spanner to push against the freely-moving piston and squeeze the lever a few times to push the sticky one out. Lube the sides of the piston with a neutral silicon lube, then use your spanner to push both pistons back in. Give a few more squeezes to ensure the pistons are moving evenly, then push them back & refit the pads & wheel. Pump brakes to reset pad clearance against rotor.
I have previously tried to align them by clamping the brakes on and loosening the various allen bolts and re-tightening them.
Loosen the bolts before clamping the brake on; that way the caliper is allowed to float around when brake pressure is applied.
Note: Hayes Sole brakes are a single-piston hydraulic, so setup is similar to mechanical brakes. The right (inner) pad needs periodic adjustment to compensate for wear. Undo the securing grubscrew in th top of the caliper (2mm allen key), then wind the backing plate in until the pad face is proud of the caliper face. The right side gap can also be adjusted by winding the piston in or out ith a 5mm allen key.
The cones can be replaced individually. It's recommended to replace the bearings as well, because it's probable that they're also pitted.