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i had the same problem when i put my Alpine IVA in my car. i didn't use the rca outputs to run my speakers. just tapped into the wires from the factory amp, so we used the exisiting factory wires to receive signals. i actually changed my harness to a non-lexus one so that i can change head units like any other car without having to worry about my cutting wires.
"Save yourself the headache(now and later) and jus re-wire the whole system."
I agree with Emerald. If you change out the headunit, you might as well run two pair of wires into the doors from the dash. The SC is by far the easiest car to pull wires into the doors because of the double hinge system that leaves a huge gap. Then you can ditch the stock amps and get what you paid for.
well I figured out most of it. Everything turns on. However my power antenna doesnt turn on anymore. Anyone have any clue which wires they are or anything that has to do with the wires? I tried using that chart thing but had no clue.