2005 honda accord, noise

Let me start off by telling you everything that I have. I have a 2005 Honda Accor with the Value Package. It has the most basic radio honda offers. It has AM/FM, CD and AUX. From the radio the signal goes to a Peripheral SVEN 4. From there it goes to an MTX Thunder 800 5 channel amp. Whith just that everything worked pretty well. I had a little issue with noise that was taken care of with gain adjustment. Now with Cd and Radio the noise is barely noticeable. The problems arrived when I added my ipod to the mix. I am using an Axxess - AIP-HD03-ID to connect my ipod is connected to the system. This enables me to use the AUX source for my ipod. Now there are two ways to hook the ipod into this device. one is a connector that goes to the ipods line out. This allows you to play and charge the ipod. When I had it hooked up this way it worked great, but the volume was very low. When I would turn up the radio louder, it would introduce hiss into the system and slight alternator whine. The other way to hook it  up is with a headphone jack. Doinfg it this way make you loss the charging feature. Moving on, I decided to put in a PAC Turbo 1 to increase the RCA level of the ipod before it hit the amp. Once again this item worked like I wanted it and gave me no problems. I am actually very happy with the way the system was operating. As we all know when you hook the ipod through it's headphone jack music tends to clip out, become tinny sound, and just be generally bad. With that I went and got a cable fron Apple that has RCA left, right, and video (video not used) that goes to the line on the bottom of the ipod. This cable also has a USB for charging.

Here is where the major problem is.

When I plug the USB into my cigarette lighter charger and play the ipod, I get this high pitched warbeling whine that goes along with the alternator. If I unplug the charger the noise goes away. Please help me, I am getting tired of dealing with this and I just want to enjoy the music, but at the same time make it sound halfway decent. Is this just a pipe dream to have it hooked up this way an make it work right, or do I need to just bite the bullet and go back to using the headphone jack?

Please help.