Heya Luke, sounds like a nice ride you've got there.
Is the whine coming from your alternator or from your speakers?
If it's from the alt, then you need to upgrade to a more powerful alternator and a larger capacity battery.
If it's from the speakers, especially from the mids and tweeters, then it's probably residual AC current from the alt causing the noise.
There are a few things you can do for this.
1. As it's been said, make sure you have a good ground. A good test for this is to make up a jumper wire, clip it to the neg terminal of the battery then to the amp and see if the noise changes.
2. Make sure your power wires and your audio wires are separated by at least 8 inches. Better yet run them on opposite sides of the vehicle.
3. Also make sure none of the wires are run along side any other wires (EMF) for any long lengths. Try to cross any other power wires at 90 degree angles if possible.
4. Keep all wires away from any electrical motors, plug wires, coil, distributor and any relays.
5. Finally, you can try a
filter on your alternator output to dump that residual AC current. You can find these most anywhere, I know Crutchfield has them.
Good luck.