Success - at least as a phase 1. I ran the long cable through one of the VERY small slots behind the subwoofer compartment leading into the trunk. The challenge was that the connectors on either end of the main connector cable. So i ended up cutting the end off the CD changer interface end. There were 6 small wires soldered to a small "logic board" like connector. I was pretty apprehensive about this because it meant I would have to solder the wires back together. But I couldn't really see a simpler way. Took a fair amount of patience but I was successful. I ran the cable underneath the center console through to the front passenger foot-well. At this point I was pretty worn out (95 degrees today in Dallas) so I left it for tomorrow to finish.
The phase 2 challenge will be to figure out the best location for the box (glove box I suspect) and then figure out how to run the iPod cable behind the radio to the drivers side where I'd like to run it into the unused accessory faceplate. I fear this will be a bit more tedious than I'd like. A bit more disassembly than I'm initially comfortable with.
Bottom line - it works. Great to be able to use my iPod and my iPhone through the radio. That alone improved the quality of the sound. The JL Audio Amp will surely improve things further. That's next weekends project.