stock unit has 6. as you noted, 3 yellow, a brown, a white, and a black/yel.
the 3 yellow go to the stator. the black/yel is the chassis ground. I dont remember which the brown and white are, and I dont have a wiring diagram in front of me right now.
I *THINK* the brown is a 'sense' wire (feedback to the regulator to control output), and white is the positive feed to the rest of the system (battery and other loads)
if my memory is correct, and the white wire is positive to the rest of the bike, and its burning up, then you have a short somewhere in the wiring or a shot battery