Hey fellas,
After having a long chat with a very knowledgeable Best Buy audio guy (rare, I know,) I learned that there is a wiring harness that allows you to straight up bypass the stock amp, with the plugs that go into the stock amp. Turns out, the info was correct, and I have found the item in question:
Metra TurboWires 70-8117 for Toyota Amp Bypass Harness 2004
This harness clips into the stock one, plug and play, and terminates into long strands of individual wires, good for wiring up a new amp to power your stock speakers. With the harness, you won't have to rewire the car or splice the old harness and risk messing up, everything is color coded.
Just thought I'd share the info, since I know many people want to bypass the stock amp, trouble free, myself included.