I took my bike to the LBS and had them mount the disc brake and the fender mount since it wouldn't easily fit on my bike. It came back working relatively well but it is a complex rear dropout on the disc brake side. The brakes still need to be adjusted, but at least the Planet Bike 60mm fender does not rub on the wire any more.
To show you what I mean, look at the picture below!
The red circle is the Avid BB5. The wires coming in from the top are the fender mounts. The Black rubber tipped piece is the Topeak Expedition rear rack. The Avid disc rotor is the scalloped shiny metal piece near the back. The motor is the last item in the background. You can see the motor power and phase wires coming out of the axle near the bottom of the picture. Amazing that it all fits!