Well, did you read through those PDF files I linked in the FAQ? Those have a lot of details to go through. Go through those carefully, one step at a time. Some of what you're describing sounds like it could be due to ground loops, and those PDF files will help you track it down.
One thing that's often overlooked is inductive noise. The audio cables are probably picking up a lot of the noise just from being in the general vicinity of other wiring. They are acting like radio antennas and picking up the noise from the car's and amplifier's power/control wires.
I recently re-routed all of my audio cables to run through the center of the car instead of the side. It helped reduce the noise I had in the system (which was very slight to begin with). As I was doing it, I discovered that even moving the cables around behind the dash would change the amont of noise in the system. Keep this in mind as you're diagnosing the problem.
Also, check to make sure there aren't any loose wires on the docking connector, or elsewhere in the system. If your wires were crimped instead of soldered, re-check all crimps. Better yet, replace all crimps with solders.
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Tony Fabris