Perhaps, pulling one sparkplug wire at a time when your engine is acting up to see if it dies or keeps running the same would be revealing? Another tip off that only one cylinder is firing, would be a comparison of the heat from your exhausts in them being the same perceived temperature or one side noticeably cooler. That your bike being as old as it is and never a problem with your CDI module is kinda rare. I keep a spare in my saddlebag, just because.
