I'm thinking a short in the left blinker wire would blow a fuse before it affected the cylinder fire.
How about a grounding issue somewhere like where all the different systems are bolt/grounded to the frame (right hand side, outboard) next to the battery?
I left one of those off when I did my battery box mod and the bike ran fine UNTIL I hit the brakes. The brake light would come on, the signal indicator would flash on, and the bike would die deader than a turd. I think the fuel indicator came on too.