hello ime having the same problem with my xj400 and although i dont now a lot about yamahas as its my first one i have been asking a lot of people who do now and the advice i have been given may help you. have you tried the alternator or dynamo wich ever yours is and also a simple thing but a very common problem ime told and that is a bad earth to the engine i hope this has helped you in some way as i now what its like to have run out of ideas hope you sort it out. corey