They BOTH go to the CDI; the RED, directly; the BLACK/WHITE through the ignition and the engine stop switches, where the conductor may be grounded to shut down the engine.
The exciter coil has two ends; when the magnets of the rotor spin past it, an alternating current is generated between these two ends. Both ends ultimately are connected to the CDI unit, where this voltage is stepped-up, rectified, and used to charge a capacitor. Each time the timing mass on the rotor passes by its pick-up coil, a voltage is induced into that coil's circuitry, firing a thyristor, discharging the capacitor into the primary windings of the ignition coil. The ignition coil transforms the capacitor voltage into thousands of volts, firing the spark plug.
That said, we're overly deep into your ignition problem, IMHO, Jim Sizemore!
Wasn't your ignition working before you began chasing these electrons to and fro?
If so, I'd again recommend examination and treatment on-hand by someone locally accessible with some knowledge of motorcycle electrics. Further exploratory surgery on your part may not produce a favorable outcome, may even be counter-productive. Yet, your bike, your call. With the unlimited possibilities, I feel frustrated in offering assistance. Wish I could be more helpful.