My advice is to break out a test light and check for voltage where it shouldn't be. If you have a multimeter with a continuity tester (the setting that beeps when you touch the probes together) you can disconnect the battery and start removing power wires until you find one that is shorted to ground causing your fuse to fail.
I would be looking very closey at the starter connections, starter relay wiring (is the NSS accidentally hooked to power?), and of course ensure the case of the alternator does not have continuity to the main power post. For safety sake check for voltage with battery hooked up, check continuity with everything unhooked.
Why are there three wires from the starter? There should be one for the solenoid and the main cable to the battery.