is this what you mean?
To summerize -- You're car audio system has two parts, a cd changer and the actual audio player. The cd changer swaps discs, plays the discs, and sends the analog audio to the audio player through it's aux ports. And, based on the links you gave, the two devices communicate via a serial protocol. You want to ditch the cd charger and plug in your own device to play music, like an mp3 player.
But, the problem is that when you disconnect the cd changer the system stops working because it thinks that the cd changer is gone. I suppose you want to build a device that will travel in your car that will make this happen.
I see this project having three large parts.
part 1: Making a cable that will connect to the audio player (audio player to serial port)
part 2: Using the serial port on a PC to figure out the right sequence of commands to send to the audio player
part 3: Making some portable solution. So, taking a processor and programming it to automatically do what you did in part 2
I imagine that there are going to be some pitfalls in there, but I can't predict what they are going to be.
Do you have any more specific questions?
p.s.
Reading about this somewhere, I saw that depending on the firmware version of your player there is another solution which allows you to short a couple of pins together to make this happen. I don't know what those pins are, but according to what I read, it is a hit and miss solution.