Did the checking I could without pulling out the deck, and I found that pulling just the rear left RCA plug makes 90% of the noise go away. I'm thinking there's a pinched wire and it's just radiating to the other speakers through the amp.

i still do not like how the rca's and power flip over each othere at the focal amp

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Not much I can really do about that, but I've tried running the cables free and clear around the outside and it doesn't make a difference.

i would test every chanel on amp with one rca connected (switch rcas and speakers)

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when you unplug the rca's from the head unit does the noise goes away? If you unplug the rca's from the head unit and the noise persists the next step would be to leave them unplugged from the HU and move on to the amplifier and see if the noise is gone. If the noise goes away after this step but not after the first step then you have a induced noise situation radiated noise from something that the rca's are picking up after the head unit and before the amplifier. If the noise goes away after the first check then you have a ground loop situation and there are a few ways to correct it.
1st being this is what I always try first is run a twisted pair of 12-16 gauge primary wires from the power and groung of the amplifier to supply all power for the head unit you will need a relay to supply acc off of this new power source and will have to doide across the coil to prevent popping. This will ensure that the headunit and amplifier have as close as possible the same operating voltage between them eliminating voltage being carried through the rca's to make up the difference.
2nd a line driver of some sort that has a ground isolation curcuit eg Audio control overdrive or matrix this will isolate the ground circutry on the preamp section input and output of the HU and amplifier thus eliminating potential fore a ground loop situation (this also has other great benifits for the system as well in terms of sound quality). These two are also great to do together.
3d and least favourable by me is a ground loop isolator.

Hope this helps

I had a simialr problem that your having on my van. I went from a alpine dvd to a pioneer filp out and the alternator whine was very little to unbearable with the pioneer. The pioneer was new too. I tried another deck which was pioneer and did the same. I changed everything to everything, but no luck. Then I tried a kenwood 5v preout dvd. viola-no more whine what so ever. So don't waste you time on trying to figure it out, just try diffrent brand deck, preferably kenwood, and I bet you loose the whine.

I yanked everything apart in the dash when I had a few seconds tonight, and found that if I pull all the RCAs from the deck, but leave even one plugged into the 4.75 amp, I get noise. I'm fairly confident I'm getting noise in the RCA's from somewhere because if I pull all the RCA's I get no noise at all.

^ That makes the deck the culprit, not the cables. With the deck disconnected the system is quiet.

Ground the outer shield of the RCAs coming out of the deck or get a different one.

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that doesnt mean the deck is for sure the culprit
that means there is also a possibility of a ground loop issue although some head units are better than others at dealing with that

So have you tried a different brand cd player yet? You could have solved this days ago had you done so. Disconnect all rca cables from the amp and the cd player. Take a meter and check to see if any one of the rca cables is dead shorting between the + and - on the cable. Then check to see if the cable is dead shorting to ground. If the answer is no (and I suspect it is), the issue is 100% the cd player.