1989 Yamaha Enticer Ignition Wiring problem

I have a 1989 Enticer 400 T/R and a 340 Ovation that have under 500 kms - they ran only one year then sat in garage. I rebuilt Enticer engine as it was stuck, carbs on both sleds and they ran great for one year. Entice 400T/R lost fire on an outing, it shut off as if key had been turned off - no spark at plugs. I have tried the following;
1. Traded CDI, magneto and external coil with Ovation - the Enticer did not start with Ovation parts and the Ovation ran with the Enticer parts so there is no problem with the major ignition parts.
2. Disconnected carb switch and joined the wires running to the carb switch to bypass it.
3. Tested kill switch, ignition and throttle switch with meter. They appear to function. Joined wires from throttle switch to bypass it.
4. I have a wiring diagram that I followed when tracing wires and testing with an ohmmeter.
5. Disconnected brown wire from CDI to magneto coil, replaced it with a wire running directly between them outside of harness. The Enticer started - however neither the kill switch or ignition switch will turn the engine of.

I plan to run wires directly from the kill switch and the ignition to the appropriate wires from the cdi. I understand that the switches ground the cdi to stop engine. Is there a possibility of damaging the CDI by doing this. It appears that there may a short or corrosion in the wiring harness???

Any suggestions would be greatly appreciated.

1989 Yamaha Enticer Ignition Wiring problem