What colors are the wires that you are not using. Did you try just connecting the wires in my previuos message right at the plug? Your switch might not make the proper connections. I sure hope you didn't fry your CDI box. I just bought one for my bike at $340. Thats not something I want to do again.
The ignition switch for the DR connects three pairs in the on position. They are - (Red to Orange), (Orange/Yellow tracer to Black/White tracer), (Gray to Brown). You might be able to connect the gray and brown wires permanently, and use the ignition for the others. Make sure that your switch for the GS doesn't connect all the wires together. That could reverse the polarity of the O/y wire (used for a ground) and fry your CDI unit. Good luck. Craig