This is not a car stereo forum, but to provide the cabling you're asking for simply involves purchasing a $20 car charger for your phone at the Apple Store and then buying a 3.5mm stereo cable for about $5 at radioshack. If you're set on having a single connector (only at the bottom), then disassemble a dock (which has an audio out) or modify it so that you have a solid place to insert the phone -- since you seem willing to do some electrical work on the car to get this to work, I'd go this route.
Personally, though, I would not want to direct-connect the iphone to a car amp. You have no control over the amplifier -- it would be always-on, including when you pulled the phone to leave your car. The better option is to simply purchase one of those Pioneer headunits and then using the integrated ipod adapter (one compatible with USB charging). If you want to only see the iPod, have the headunit moved to the glove box or under the passenger seat, and then only run the adapter cables to the instrument cluster, buy a horizontal mount, and just clip the phone in -- voila, "iphone" headunit!
Whatever you end up doing, good luck,
Josh