Well, after 3 years, I've finally gotten rid of the alternator whine.

All it took was me accidently blowing the amps (errr I need to mind B+ and GND)

I had them repaired (for free ) and when I got them back, and reinstalled them, no further alternator whine exists. I'm almost positive that there was a problem with the amps from the get go (which a few people here suggested).

In the process I also upgraded to 16G speaker wire all the way around (from 18G) which really improved how the car sounds as well.

Now, since i've been without music for 3 weeks, I'm in the process of upgrading to 3.0a5, the latest version of hijack, and loading some new tunes