the brakes run on a separate coil because the power out of the coil is continuous and runs to the brakelight and also to the switches where it is dumped to frame ground. when you pull the lever it breaks the ground and lights the taillight.
at any rate, what i'd do is get the bike running and idling, take a voltage tester like this (cheap like under 5 bucks at auto or hardware store)
and test the wires directly out of the stator (and disconnected from everything else.
plug em back in and test again until you identify at which point power is lost.