You may want to us an ammeter to test the amperage output from the alt with a load on the system. You could be getting a good voltage reading if the regulator is working but the alternator may not be putting out any amperage.
I just installed the same amp and have the same problem. I regrounded all my amps and HU and still get a slight whine when my lights are on. I leave the interior speakers on flat at about 1/2 gain and keep the low freq setting on the head unit at about +3dB (+9dB being the max setting) and I do...