Alternator whine in a 92 Civic

I got a 92 Civic Si hatch. The alternator in it is about 6 months old (not saying it's not the problem as i have yet to try a different one... but the problem started after a few months of it being in). I have a Pioneer P80MP, ground is to the chassis of the car, the constant 12v is direct from the battery and the switched power wire comes from the fuse box. I have 4 gauge ground to the chassis using a PG gold negative battery connector. 4 guage running to 2 amps using distrobution blocks on positive and ground. Rockford 500x 4 channel... all speaker wire and RCA's are BRAND NEW with every connection at the speaker being soldered on. My ground in the back is excellent, also 4 gauge.

Now i'm trying to figure out why i have alternator whine. It's not only alternator whine though because the more loads i put on, the louder it get's... also when i use my turn signals i get like a clicking sound out of the speakers, most likely from the tone of the alternator whine changing due to different loads on the system. Is the problem most likely my alternator as i've changed every wire that has to do with my stereo or could the problem be maybee in the switched power wire on my deck being shorted in the fuse box somewhere ? I've tried ground loop isolators, 1 per set of RCA's, i have 3 sets of PG's. This is driving me nuts. I've tried disconnecting the alternator completely and starting the car, I don't get a whine but still get the clicking sounds i described when i use my turn signals and turn on and off different loads. When the car is running and i have the amp connected... the whine goes away when i disconnect the RCA's... so it's not the amp. Also, the whine is more noticeable from my 500x, and not from my sub amp being a Kenwood, although it pops really loud when i turn the volume from 0 to 1...

Please help... this is driving me nuts, sorry bout the long post, i just wanted to try and put up all the info that would be needed all in 1 shot.

Well if all your wiring is properly hooked up. The only thing that I can think of is that your alternator is straining to power all your electronics. Ever think of upgrading your alternator?

try grounding ur rca's...not using a ground loop isolator.....from behind ur Headunit,...wrap a bare wire around all ur rca's and ground it to a clean ground that is not being shared...if u hear more whine...switch the ground....if that doesnot work....are u amps mounted on wood or metal....if metal u have to put a piece of wood between the metal and the amp.....let  me know wut happens

Here's something I forgot to add... the system ran problem free ever since i've had it. The "big 3" were already done to the car b4 my current install. I'm gonna try grounding out the RCA's... that's about the only thing I can think of rather then my deck went for a crap (never know with pioneer), or my diodes in my alt are gone.

I'm having the alternator checked out today... will see how that turns out.

Well I installed a brand new alternator today and the alt. whine is still there... damn i love lookin for ground loops... i've regrounded everything properly...

Think maybee the deck is shot even though it's only 5 months old... i mean it did work fine for 2 1/2 months... lol

My estimated guess is a poor circuit design in the Pioneer cd player. In particular the ground plane. If you have not tried muting plugs yet, make some. Take an el-cheapo rca cable and cut the ends off. Wire the center conductor to the outer conductor. Plug into the amplifier. Do this to all 4 inputs. Do you still have noise? Unmount the amplifier and place it on cardboard, do you still have noise?