electrical fault Yamaha Virago 125 1999?

you say it runs ok so that rules out the cdi, if fuses are definitely ok and the contacts are clean and bright then there must be a break or short somewhere in the wiring, follow the wiring from fuse box to inside headlight and handlebar switchgear, a break inside the wiring is less obvious but if you used a multimeter to test the fuses then use that to test continuity, just a case of looking carefully and checking that all connections are clean and tight.

Grizwold
June 2016