Clutching at straws here, but you say the problem only happens when the fan kicks in. I know you disconnected the fan etc. but where abouts? Before or after the relay? Did you pull the plug to the fan or pull the fuse? Perhaps pull the fuse and then test, careful not to overheat the bike of course.

I know on my XTX everything starts to get a bit vibratey around 5,500rpm... maybe there's a damaged/rubbing wire and vibrations are disturbing it, maybe shorting on the frame?