Ok, a few other extremes I have done in the past.... I totally isolated the HU from and ground or power source at the front of the car. HOW?
1)- Depending on how your HU is installed your gonna have to get creative and make sure no part of the HU or the sleeve touches ANY metal in the dash..this includes the rear support bracket... your on your own here.. there are a million differnet ways to do this.
2) - I ran new power wire (8GA--because I'm only using line outs, no amping required at the deck) from the dist block and common ground block in my trunk to the dash. At the dash I split the two power wires, One to the constant (yellow or orange lead depending on make) and one to simple Radio shack 12 volt, normally open relay. Power in, power out.... then use the factory wire from the fuse panel to trip the relay. DO NOT Ground the relay ground to the same place as the HU ground tho! You will defeat the whole purpose.
3)- It cannot be said enough... USE SHEILDED or Twisted pair RCA's for the run to the back and if your head unit doesn't do it, get a line amp and jack up the power to at LEAST 4V before running it to the trunk. Amps, crossover, whatever. the higher the output the less likely you will inherit nose from other sources like computers, harnesses, etc in the car.
4)- It should seem obvious, but if it is alternator whine you are dealing with you Should go right to the source. You may consider replacing the Alternator diode bank (that little circuit board on the back where the removabele panel is.. depending on what kind of alternator you use of course, and also replace and reground the regulator--usually located on the firewall or in newer cars under on of the many plastic boxes under the hood.
DO THE BIG THREE... Ground ground ground... make sure other primary electrical components are properly grounded as well... accessories, aux lites, if the sound only happens when you use the brakes (pops and clicks) then check all the relays in the braking system, when your lights are on? When you roll up/down electric windows...
This kind of troubleshooting is all about isolating the bad ground and replacing it. The reason you get the whine/noise is because something is improperly connected or loose and that "source" is "borrowing" (if you will) from your sound system,....the most obvious way that you Hear it before it appears somewhere else.
There is obviously a LOT more to this... it is just gonna take some work and patience. Start isolating stuff..