I have a 2003 1100 custom that has always had some sort of issue with excessive wear on the rear brake pads and rotor.
I have replaced 3 rotors, 4 sets of (OEM) pads, a rear caliper assembly and have also rebuilt the master cylinder.

What happens is that the brake pads wear down to the substrate metal on as little as 1000 miles.
No, I'm NOT using it as a foot rest lol.
But I'm drawing a blank here...

One thing,
This bike has Double D exhaust pipes and has been re-jetted for this.

The only thing I can think of is MAYBE heat from the pipe is affecting the master cylinder and causing the fluid to expand and compress the calipers.
To fix this, I might add some sort of heat shield, or relocate the master cylinder to a cooler spot on the bike. Heat shield-easy if it works, cylinder relocation, no so easy.

What I'd like to know is has anyone else experienced this sort of problem?

WinchDoc

first how close ist the exhaust to your caliper? second 1000 miles ouch dude! ive got an after market exhaust also and i dont have any trouble. i use my rear brake as my primary and the front to added braking when needed. check you brake line after the cylinder, mine has a heat shield on it about six inches long. might be that you rear brake cylinder is not releasing the pressure after you release the brake and that may be causing the excessive brake wear your pads should be a little loose. check when the bike is cold and hot and compare. good luck