Since you already replaced the CDI box, that eliminates the CDI box as a possible source of your problem. That leaves the wiring along the battery>ignition switch>kill switch>CDI box as the possible source of the problem. I think you could perform a simple test using a temporary wire that will help get to the bottom of this. The CDI box has two connectors. One has 4 wires and the other has two. On the two-wire connector, the wire colors seem to be green, and brown/yellow (my copy of your wiring diagram is hard to read, so I might have those colors wrong). Anyway, leave the connector plugged into the CDI, and jam one end of a temporary wire into the back of the brown/yellow wire portion of that connector. Attach the other end of the temporary wire to a point that has battery voltage. You could even attach it right to the + terminal of the battery if that is convenient. Now run your machine. If your problem goes away, then you can consider this test to be proof that your problem is caused by a bad/intermittent connection somewhere along the battery>ignition switch>kill switch>CDI box.
Note: When you have the temporary wire in place, the machine won't shut off just by turning off the key or kill switch. You will need to disconnect the temporary wire from the battery voltage point and then turn off the key.
