Alternator whine is caused by a ground loop in the wiring system somewhere. You did good by running on opposite sides of the car. Ground loops can enter almost anywhere, at any componet. Having many ground points on your equipment is a perfect cause too. Try and have all your grounds as close to eachother as you can. Anything up front you have, ground that together, and the amps in the back, ground that to baremetal, with a bolt. Also, try cleaning the battery-to-chassis ground at the fender, be sure its on bare, clean metal. If the noise is still there, try using a "twisted pair" type of RCA connector, as these will null out any possibility of induced noise picked up along the run of the RCA cables. Do you have an amp going to your fronts and rears? If you do, run the car to make the noise, then disconnect the rca inputs the amp that runs your fronts/rears. If the noise goes away, then the ground loop is entering through the RCA, most likely at the head unit, by bad grounding. If the noise is still there, then its coming in through the power wire, but thats less likely. Also, a WEAK or BAD battery can let alternator noise in to the power wire for an amp. A good, fully charged battery will itself "filter" out most alternator noise. I have a yellow top battery, 3 amps, and power wire and RCA down sep sides of the car, and a bolted ground in the back for the amps, and NO noise whatsoever.

13.5 @108 MPH-2.2 60ft(stupid FWD!)
S16G @ 18 PSI/FMIC/Running on MegaSquirt II (Now with sequential
fuel injection)
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-1998 Mitsubishi Eclipse RS-T- "Toy"
-1992 Plymouth Laser Turbo AWD(SOLD)
-2000 Honda CR-V(daily)