I've been re-reading this thread, and a thought just popped into my head; you say you arent getting any braking because travel is too limited. Have you also adjusted the brake rod arm (connects at rear wheel, spring tensioned on the rod that connects to the actuator) to test that you have brakes?
To do this, raise the rear wheel (center stand, lift, wheel chock) and spin the wheel. Then manually move the brake arm at the rear wheel. This should stop the wheel. Please confirm this portion is working, then we can continue on the travel/pipe conflict.
*the reason I'm asking! you should get some braking pretty quickly with the arm! even though there's conflict. The nut at the rear of your pic actually prevents the arm from being pulled too far back by the return spring. The should be a limiter farther forward to prevent over-travel, perhaps in front of the lower engine hangar bolt? Or your return spring (coil wrapped around the arm and pinned to frame) will return the arm to de-brake, if you will. That's where the limiter nut comes in...