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My truck is an '04. The wires you're seeing to the left of the footwell, near the emergency brake pedal go through the firewall. They are there for use if adding accessories. They are not the brake controller wires.
As already stated, the connector for the brake controller is under the radio area. It isn't actually 'under the radio'. Rather, it is pretty close to the bottom of the dash - really it is under the 'cubby'. If you take out the large plastic panel under the steering wheel, it is easier to see.
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