My 98 F3 did a similar thing. It ate a couple of fuses intermittently then died all together. It turned out to be a terminal block by the instrument cluster that had corroded to a point of shorting out.
I would look carefully at each connection starting at the front and working to the back. Also look for areas where the wire harness passes over frame or other metal parts. Look for damaged insulation.
Finally take your battery out and while it is being charged (off the bike) use an ohm meter to trace the wire from the B+ to the fuse block. Take out the fuses and keep looking for a short to ground. Most electrical devices on the bike will have at least a few ohms of resistance. However, a short will likely have no resistance. Isolate sections by disconnecting both ends when possible.
A schematic of the electrical system for your bike will help too. Service manuals have them in the back. Be patient. You may find the problem quickly or it may take hours.
Good luck.
mikey