After looking at the wiring diagram, and based on the info that the horn and turn signals work, but the front and rear brake switches do activate the either brake lights, it sounds like a wiring harness issue.
Does this bike have an aftermarket undertail/lighting system?
The problem could be originating at that point.
If it's OEM light assembly, then I'd check if you have voltage at the brake light sockets between the G/Y and G wiring. Then start back-tracking.
Last edited by SubSailor; 09-25-2014 at 03:37 PM.