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This sounds like your charging system is not doing its job. You were running on battery power alone and just drained the battery until it would no longer run the fuel pump. The ECU requires a minimum voltage, not sure where the cutoff is. Charge the battery, crank up the bike and check the voltage. You should see about 14V when the engine is spinning at 3500 rpm. I'm sure a 'real' engineer will have even better suggestions but that's my best guess.
@Bulldog9The bike was not losing power just shutting off directly, mostly when I would make a slow turn and engage the clutch so the revs would drop to neutral. Then I could start it again (till it finally died in front of my garage). But it felt like it needed revs and the engine to be engaged to get the electrical power going.
Am I missing something here.....If you waggle the handlebars and the connection is good / bad it shows it is NOT the ignition switch but is a wire or connector. It could be a connector on the ignition switch but not the switch itself.AndyB