The blue-wire from the three prong flasher socket seems to be tripping the fans to come on. Any idea how this could happen?
Sounds like you have a short between circuits (insulation gone from both wires and the copper touching.) A rewire should fix that.
Joe's idea of using a relay to isolate the heavy load from the ignition switch is a good one. Pretty easy to do. If needed you could run a separate heavy gauge wire from the Starter terminal (with a fuse) to the relay, but the Amp gauge as a source should work OK. If you're still running the 6V wiring, the gauge should be good, as using 12V on the same load originally run on 6V only draws half the amps.
