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Temporarily mounting something like this might tell you a lot ?https://www.amazon.co.uk/XCSOURCE-Motorcycle-Waterproof-Digital-Voltmeter/dp/B01NAK5ENF
My money would be on the rectifier. Intermittent misfiring suggests the alternator putting AC into the system, especially when the rectifier gets hot.A typical sign would be a cooked battery making you think the battery is at fault. Check battery electrolyte to see if its been boiling.Its worth checking the rectifier connector block which may be corroded causing a high resistance. Gareth.