I'm not sure if you've gotten your install squared away yet, but it sounds like you might need a MITAH box. Check out the Club 3G fourms at www.neweclipse.org if you haven't already for more info.

I have some pictures of my dual head unit install in my 2k GT on yahoo at http://photos.yahoo.com/kryworuka I have none of the factory stereo though, so it's not really the same situation as yours.

Steve