A question that might seem unrelated: are you using the glass fuses, still?
Reason I ask: the type of fuse needed is the SFE. This looks like a wide piece of tinfoil inside the glass tube. They have not been made at all since 2002. Only a few were made after 1997. The ones you get now are instrument-grade, or if using the ceramic-case type they are appliance grade, neither made to operate with vibration. When they carry current they get soft and flexible, and a bump can break them at that moment, making them look like they "blew" for no apparent reason.
Here is what complicates this: the clips on the fuseholder are (were) plated with chromate, which was a 10-year life product. Today it has lost its grip on the metal clips, and it makes an effective heater when the fuse passes current to it. This heats the weak fuse even more, and makes them melt easily.
Here's how you can test if yours is causing 'blows' for no apparent reason: if you have a gun-bore brass cleaning brush in .22 caliber size, or one of the small round metal brushes form the Harbor Freight assortment of brushes, spin it inside the fuse clips to clean away the chromate plating that is falling off now. When it shines again, reinstall a fuse and try your tests again. There might not even be anything wrong with the bike itself.
If that solves it, I can make a new fuseholder for you that uses modern ATC/ATO blade fuses, which will let you find the correct fuses everywhere (even the grocery store!).