Ok, alternator whine is a TOUGH beast to deal with. First and formost, is your power wire from the battery anywhere near your alternator. You want to keep that bastard very far away from the alternator. The reason you get your whine is the magnetic field put off my the alt affects the power cable, and subsequently causes a current. This slight current is then amplified by your head unit/amplifier and you get what I referred to on my Toyota as a "fake turbo". There's a few ways to combat this, first, easiest, but probably most expensive is to go ahead and drop bank on shielded wiring (Monster Cable works great). This has a special insulator that prevents the magnetic field from showing up in your speakers. Second, and still pretty effective is to install a high pass filter going to the errant speakers. I am not sure of your speaker/wire/amp/head unit setup, so I can't give you much more than general help. Hopefully something in here was useful to you, and good luck dealing with that whine, I never could completely get rid of mine in the Yota.
