[GMo]

Alternator whine wouldn't be happening due to RCA's and power wires running too close with DC.

So, you have the amp(s) disconnected from the signal (RCA's) and still have whine...can you pinpoint the source of the noise? Have you had problems with your alternator? Have you been having problems with your battery?
I would have both of them tested if you can't figure this out, and I believe places like pepboys do it for free. You can use a multimeter or voltmeter on your battery to see if that's functioning correctly.

Anything which outputs pulse width modulation (computers. lights, amps, HU) can be causing the alt whine . It can be heard through any speaker which doesn't have a high pass filter under the audible frequency. I've seen aftermarket alarms causing it. If your HU is still connected to a speaker it could be causing it.

No matter what I would re-do your grounds, like I've previously explained. Check your battery for a proper voltage- whatever it's spec'd at , 12.6V or around there, and for a proper charging voltage, around 14V. If your battery is failing or cycled down, it could be the culprit.