The secret is in the wiring harness.... I started with some basic questions about how the CDI do their internal timing ignition advance and how they regulate the outgoing "trigger" voltage to the coil. These led me to a MASSIVE black hole which is the CDI box and how yamaha manufactured it. Basically there's NO information on how it's made or how it works so I came up with a work around.
Knowing that each ignition system has 5 main parts (read : necessary) I worked backwards to the CDI box instead of from inside it. Those main parts are: source coil, trigger coil, CDI, kill switch, and ignition coil. Those all have to work together to get the power in and power out at the exact right time (and finally to stop the power when you want to LOL)
Knowing each CDI is "fed" power from a source coil I began to look at the stator plate. I noticed that except for thickness (and mounting post height due to that thickness) the source and lighting coil look identical. I cut two thin aluminum "washers" and installed another source coil where the lighting coil was and hooked the second source up to the lighting coil wire on the stator plate.
Once into the "main harness" I ran both source coil wires to the front, both orange ignition coil wires to the back and then branched the trigger coil wire and the ground coming off the stator plate into each CDI box. If everything works according to plan both CDI's will "see" the timing (according to the trigger coil) at the same time and run parallel ignition timing curves and trigger their own coil at exactly the same moment. I even took the extra steps of making the orange ignition coil driver wires the exact same length and the trigger coil wires after the branch the exact same length.... just in case.
That's as good as a po' boy can do for running twin ignition systems. If this doesn't work (which it should but just sayin'), it's back to the drawing board to figure out how to stack two trigger coils.... or perhaps I'll just skip that step and go straight to COP (coil-on-plug) and an aftermarket ignition driver box. Who knows!