OK..Here goes!
I have a brand new 150amp Mr. Alternator with 4 gauge wire. I re-did all of my under-the-hood wires as well. I now have my head unit powered and grounded directly to the battery. I have BAD alternator whine and tick!!!

If I unhook the RCA's from the the amp, the noise stops..so the noise is coming before the amp. Anybody know what's up?

Also..I have this freaky problem with my ipod charger. If I plug it into the factory cigarette socket, it works perfectly. BUT, if it's plugged into the socket I installed behind the dash, it freezes the iPod as soon as I plug it in. This started happening after I repowered/grounded the head unit tonight...

 

For the whine, you can get a ground loop isolator.
http://www.crutchfield.com/S-xs0qP5F...ch=ground+loop

 

Did you run your RCA's and power down the same side of the car?

 

Ahh..I had them installed "professionally" for free because of the flooding issue after my alarm install. The power wire runs along the driver's edge..while the RCA's run under the console. At one point, the RCA's for the subs cross over the power wire..but not the two sets of RCA's for the speakers. Is that 2' of space enough to stop the noise?


Also..I was fooling around with it today and completely unhooked the ground going to the battery. The head unit kept working, and the noise lessened. So I'm guessing the unit it getting a ground from it's chassis to the dash. Bad?

 

Its best to have to RCA's run completely away from your power wires. You get interference from the power wire. In mine, the power is run down the drivers side and the RCA's go down the passenger side and never cross or get near the power wire. If you have some spare time you might want to consider moving the RCA's to the passenger side and try to make them where they dont intersect the power wire in any way.

 

If you have a separate set of RCAs, you can run them over the console to the back. If you still have the whine, you can rule out interference and leave your existing RCAs in place.

I had the same problem in my other car (accord). What I had to do was actually ground my RCA Cable. For some reason, my HU->AMP wasn't grounding correctly. The instant I hooked a grounded wire to the outer sheath of one of my RCA cables, the noise stopped. To test this theory, add a ground wire from the HU ground (make a 3 way splice) then run your new ground and touch your wire to the outside of your RCA Connection at the back of the HU. IF the noise stops, you'll need to permanently attach this ground to your RCA wire.

I spliced into my RCA sheath exposing the metal wrap around the inner core. I wrapped my ground wire around the metal wrap and taped it up. Problem solved.