the amp is in the trunk on the Passenger side, there is a whole manual on how to get to it - don't try without reading it or you'll break a bunch of plastic...
and yes it's 2 wires + shielding that you need to get through.
Some searching and I have found where it is:
How to Remove the Navigation ECU from a 2003 Toyota 4Runner
now i need to find the wiring diagram. lastly I hope that 20ft of shielded stereo cable from Radio shack should do the trick.
Have you done this?