I guess you just need to start with the basics and work forwards. The problem as you know is replicating the conditions. If it was me (and all advice/opinions given on the internet are without guarantees and taken at your own risk!!) I would start at the battery and just work forward though the electrics just cleaning everything up along the way. May want to use dielectric grease on electrical contacts (Silicon based) which will work longer than WD40. Doesn't sound like the sidestand cutout if it was running on one cylinder before. Does the Bonnie have a neutral or clutch cutout safety switch as well?
