So depending on the gain setting on the amp, if I have it down to the lowest/min setting, then the alternator whine noise is only noticable if the head unit is on and the volume is at the point where there is no sound through the speakers (less than 30). With this setting (gain set to lowest level on the amp), the music volume has to be turned up pretty high on the head unit to achieve acceptable music volume for driving conditions (greater than 50; and the max on the head unit is already 65). I don't like this as I want to be able to go up/down depending on use (though most of the time it would just be set at average listening level).

Yeah, I tried the ground loop isolator on the RCA cables and that did not really help. I'm trying a power line filter next. Have you tried a power line filter on the yellow cable and the red cable on the Fakra?

Regarding your grounding from the head unit, are you grounding it directly from the head unit's frame? Or are you splicing into the black wire of the Fakra cable at the point where it is leading into the head unit?

For the passive crossovers, I got them for $18/ea on eBay (AUDIOPIPE 500 WATT PASSIVE 3-WAY 4ohm CROSSOVER NETWORK | eBay)