The radiator fan relay is in the fuse box under the hood, near the stock ECU. The wire you're looking for is a green wire with an orange tracer. When this wire is grounded by the stock ECU, the radiator fan is activated at its higher speed. Simply clip the wire and connect the end leading to the relay to the wire in your Megasquirt harness.

Download a copy of the electrical guide for future reference:

http://www.symtechlabs.com/downloads/dl.php