If someone can provide the schematic of Bose sound system for 2000 and older model, I should be able to figure out the connections for your ipod. You will have to split the audio signal output of your Bose radio before it reaches amplifiers, install DPDT (double pole double throw) switch anywhere under dash to flip between audio signal from ipod and radio unit. Volume on your ipod will control the aplification (I'm not sure what levels it will go to, how loud it would get).
You may be able to do this trick to CD changer audio output signal wires, leave one CD in it to cycle the unit on so the system knows that CD it playing but feed ipod audio signal into stereo head unit instead by use of DPDT toggle switch to be able to switch back and forth between ipod and CD changer at any time.
I'm pretty sure Witek or 43sqd could come up with wiring diagram for CD changer connector.
Long time ago, when I was still young, I used to install LED audio dB level indicators into cars, same as you see on old home theater dual cassette players, equilizers or aplifiers. 12 to 20 LEDs for each stereo channel and when the basses hit, your car would light up inside from yellow, green to red. Or you could have only one LED on at a time going through the audio level scale back and forth without too much light showen.
Most people wanted them lid all (like a Christmas tree), I could not make enogh of them.
The main thing was to find the correct audio signal wires to hook up into stereo system.