Anybody reading about this in the future the harness provided on the radio people were having trouble with is actually not wired correctly for a 2004 that's why the sub isn't working. The polarity of the front left and rear right are reversed. To make the factory sub work you need to switch pins C2/C3 and also C13/C14. After this swap it'll work fine. The speaker polarity from the ground side needs to go + - - + and not - + - +.
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For those that are using an external sub with the factory speakers powered by the deck you still might consider the swap. The speakers would be out of phase.