[SwingBringsPain]

Brockoli,
I had this same issue. The way I solved it was I looked on Craig's List and searched for Car Audio install services. I found a kid about 10 miles away who said he could fix anything, and install anything car-audio-related. He ended up installing a ground loop isolator and it fixed the whine 100%. He charged me $40.

What you have is called "Alternator Whine" or "Auxillary Input Whine." It has to do with how the stereo is grounded. I suggest finding a car audio guru in your area and asking him if he can fix alternator whine. It's a simple, cheap fix, but you'll spend a ton if you go to a "Pro" audio shop.