Looking at the wiring diagram in #15 of Rostra Cruise Control Alternate Wiring, it sounds like there could be a lead shorting to an earth / frame somewhere and thus causing the fuse to blow while the ignition is turned on / engine running. The live for the cooling fan fuse is traced from the ignition switch, starter button and horn via the orange lead. Any electrical work done in this area?
With the fan disconnected and the ignition turned on / bike engine running, does the cooling fan fan fuse blow?
With the fan disconnected and the ignition turned on / bike engine running, does the cooling fan fan fuse blow?