I've been told that the connection on the front of the Shaker 1000 system integrates to the earphone jack on the iPod, and the signal that is output from the earphone jack is a true digital signal.
Since my '06 V6 with the Shaker 500 system doesn't have that integration port on the front of the radio I had an integration unit intalled to the rear of the radio which has a digital input port. That connection integrates to the bottom port of the iPod, provides a true digital signal and also keeps the iPod charged in the car. The only thing I'm missing is the ability to control the iPod through the radio controls; it's my understand that the Shaker 500 radio doesn't have that capability
