Here is what I can tell from the wiring diagrams.
1. From the alternator/stator area, you should only have to worry about the black/red wire. This provides the power to the CDI.
2. The two yellow wires (per the Honda manual) or the Green and Yellow wires (per your engine) should only be for the lighting/charging circuits. They feed the regulator/rectifier. Based on the wiring diagrams, there is not a connection between the regulated DC power and the CDI, so you shouldn't need to worry about it (to just get the engine running).
3. The pulser (ignition trigger) wires are the blue/yellow and green wires. Blue/yellow should connect to the CDI. The green goes to ground.
Check all your grounds. Make sure the engine, frame, and any/all green wires all show low (zero) resistance. Especially make sure that the motor is grounded, since the power source for the CDI only runs the hot lead out, not the ground. It grounds through the engine case to the frame.
What coil is on your machine? Does it have a single wire (black/yellow)? This style grounds through the mounting flanges. Again, make sure this is clean and that you have good continuity from the metal tab on the flange to the frame to the engine and to any green wire in the harness. This is typically where the harness ground eyelet is connected. Make sure it is.
If you have the two terminal coil, then the harness ground eyelet connects somewhere else on the machine and you have a dedicated ground wire connecting to the coil. Again, check your grounds.
Last, the kill switch turns off the machine by grounding out the black/white (85) or black (84) wire from the CDI. In other words, leaving this disconnected will make sure that the CDI will fire the plug.
- Frank
1984 200ES Big Red
1985 350X (x2)
1986 350X
1986 250SX
1984 Auto-X
1984 ATC70
1985 ATC70