I think it is best to start at the basics and physically check each system start to end to track it down. I would check with a multi meter to verify the clutch switch is working. Then make sure the ignition switch is indeed opening up the spark system. Then verify that there is juice from stator to pulse generator. Then check that a signal is coming out of it and going to cdi. Verify continuity to the cdi, then verify the spark signal is coming out of cdi and going to coil, then out of coil to plug.
To start, take the wire harness apart somewhat and eyeball every inch of the wires for any broken wires, lightly pull on all terminals going into connectors for broken wires. Clean all contacts and all grounds. Then proceed with system checks above.
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