OK, so here's what i've figured out thus far... if history proves to be right, then the thicker gauge wires from the stock amp in a twisted pair will be going to the subs under the front seat (see photo below)
That means Blue/red + Blue/brown and Black/red +Black/brown are going to the subs and next to those there is also a thick Red with white stripe (I'm assuming this is positive Power and the Brown is negative)
Also, if you look closely with those same wires, there is a very thin black wire... is this a remote turn on for the stock amp??
The bigger question is which wires are positive/negative and which side is right and left?
Here's a shot of the harness as well:
And if you yank back the carpet, here's all the wiring heading to the front of the car down the drivers side: