Based on what you have told us (parts from your broken bike work on your working bike) it sounds like the fault is either the CDI ignitor box, or the wiring loom between the ignitor and the not working cylinder. The CDI cannot be tested, but the wiring loom can. I am also leaning toward the wiring since your bike has been modified. Since the other cylinder is firing and both coils are on the same power circuit, that problem is in the ground circuit. Perform a continuity test between the following wires:
5plug ignitor connector - Black to
Coil1 - Black
5plug ignitor connector - Green to
Coil2 - Green
You only need to test the one that doesn't work, but the schematic does not describe which coil is on the left side, so go by the color of the wire other than the red one.
If it passes that test (continuity indicated), also check that the black wire that normally goes to the tachometer is adequately insulated from the frame and not providing a short to Coil1. To do this, unplug BOTH the CDI and Coil 1 and test for continuity between either
Coil1 - Black to
Frame or battery negative
OR
5 plug CDI/Ignitor - Black to
Frame or batter negative
If the test also passes (no continuity or infinity resistance), then swap the CDI from the 2004 and see if that works.
Also, is the inductive tachometer getting power from an extra wire you connected directly from the battery or have you spliced it into an existing power line? If you have spliced it in, what color is the wire?
