I looked at the pics of the '06 HU rear end - looks just like our '05 - nothing different. I asked the guy that I'm buying the HU from to leave the connector and a piece of wiring (he does not want to take out entire thing - does not want a hole in the center console). Anyway, if I get my HU with a piece of the harness - I'll let everybody know.
I have the wiring diagram for the regular '06 HU, but not the iPod one.
Regular one uses 4 pins on the regular HU harness to connect to the aux-in. I'd guess that iPod HU has a similar setup, maybe more wires, plus you need an iPod connector - a bit more complicated than regular aux 3.5mm jack.