Still having problems. Llast night I tried checked all the points on the docking connector and all seemed okay. I ran a direct line from the battery for power. Wire was 14 gauge which I think is thick enough for the empeg. It's a Rio Car, mk2a, purchased during the clearance sale so I don't think it has that cap.

The RCA cables I used are high quality Phoenix Gold cables and are shielded all the way around.

The noise is definetly alternator whine. The pitch gets higher when I step on the gas and totally goes away when I turn off my engine. If I turn the music up high enough, it gets drowned out, but when I have my girlfriend in the car and the volume is low, it's really annoying and I end up just turning it off.

I have a 1 Farad cap next to my amplifier, Do you think that adding a small cap to the power line of the empeg would help filter it out? I might pass by radio shack and pick up a little 1000uf cap and see if that does anything. I don't know what else to do.