I had a similar problem after removing my front wheel to transport my Jekyll. Turns out that when I put the wheel back on, the rotor wasn't centered between the pads (which seems to be the same problem as yours). All I had to do was pull the caliper off the fork, remove the brake pads, and use a box end wrench to push both pistons into the caliper. Then, when I put the pads back in and reattached the caliper, I just pumped the brake lever a few times until it was stiff and I've had no more problems (I also haven't removed the front wheel since I got a Sportworks rack).
If you've ever changed the brake pads on a car, this should be a familiar process, because they use identical self-adjusting mechanisms, meaning you shouldn't have to adjust any of the shims on the caliper except to make major adjustments. Basically, the piston is sealed to the caliper by a ring with a square cross section. When you pull the brake lever, the fluid pushes on the piston, and the seal deflects so its cross section is more of a parallelogram. If it has more space to move after that, it moves but if it bottoms out on the rotor, it will just stay there. When the lever is released, the piston is retracted by the seal returning to its square shape so the gap between the pad and the rotor will always be a constant distance. Unfortunately, it will only adjust for the gap getting bigger, while the problem you're having is from the gap being too small.
I hope this helps you.
Any setup hints for Hayes HFX 9XC branks on Jekyll 2000 w/ lefty. My lbs orginally installed the brakes for me. No problems with the rear, but the front brake developed this annoying squeak since about day one. I tried retruing the rotor...and also say that the lbs installed the rotor mount upside down. I reinstalled in the correct way and spent nearly 2 hours trying to center the caliper w/ washers, using business cards on either side of rotors for gaps... I think I have it as best as it will get...but I still have the squeak and a little drag.....
Any thoughts...the noise is driving me crazy....I guess I will keep with the trial and error process of truing the rotor and shiming the caliper.