Hey Im sure this has been done before but I figured I'd post a pic of what I did in case anyone is wondering how to keep their stock USB and AUX but be able to use them with an aftermarket HU. All I did was desolder the stock connectors from the circuit board and add a couple male connectors so that they'll plug into the HUs cable. I am using this with a Pioneer AVIC-X940bt and it works great. The best part for me is that if I want to return everything back to stock I can simply solder the stock connectors back in and be good to go. Let me know if you have any questions.
cool, I did something similar to my VW R32. It was tougher because the VW had an actual iPod dock to deal with, but yea, carefully solder each wire and it OWM dock in the arm rest worked with the Pioneer AVIC