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Go get this: http://www.logjamelectronics.com/pietoyaux.html

It will hook up the the aux connection in the back of your stock HU for the trunk mounted CD changer. It converts the connection to a right and left RCA. You can then get a male minijack to male right and left RCA cable, and hook your Ipod's headphone output to the new RCA inputs to the HU.