You also could have solved this long ago by grounding the RCA's. It's not a big deal to do...a whole lot easier than changing the deck, and it's gonna work just fine.
When it does you best be looking for the bad ground that caused the issue, because it's likely that you aren't getting the full potential from your amp(s)

 

Took it over to method acoustics and we hooked up some new RCAs to the existing HU, and lo and behold, the alternator whine stopped. So did the CD noise. There is a BARELY perceptable hiss on a 0 dB track, but you really need to have your ear to the speaker to hear it. I'm willing to chalk that up to either the hu or a crappy solder somewhere. I can't find any nicks or pinches in my (still in) RCA's, so hopefully I can get my money back for them and get some new ones.

Thanks for helping me with this! I'll post an update once I get the new cables installed and hopefully this is the end of my problems.

 

Alright, update time. Been working like a dog lately and haven't had time to do much work on anything but here goes:

I replaced all the RCA cables with better shielded Scosche cables, and while the noise did get slightly better, the alternator whine still persisted. I still have loading noise from the deck as well. My temporary fix came when I ripped out all my RCA's in a fit of rage and noticed that with the rear ones removed the whine stopped. I've just been driving around without my rear deck speakers for the last month and a bit and I can live with that. I wish I'd known it sounded this good without them, and I would have saved a few bucks and bought the FP 2.75 and left the rear deck speakers alone. Actually that would have saved several hundred dollars, but thinking about it makes me sad.

Pioneer has agreed to take another look at my deck but I have not found the time to take it in to the repair depot. Hopefully in the next week or so I'll get it pulled and into the shop. If I still can't get it resolved I will probably buy a new deck, which sucks because I love this deck. 99% sure the deck is the problem.

 

^ welcome to the world of car audio complete with 20/20 rearward vision... Still sounds like the one of rear speakers may be in electrical contact with the frame or the amp driving the rears has a connection issue (internal loss of ground on the RCA or a lousy solder joint).

 

Hey, it's time for another update! Yay! The stupid thing still doesn't work!

After making Pioneer rip the whole head unit apart and re-do the grounds, even though they were fine, still didn't fix the problem. However, when re-installing the HU, methodman and I discovered a new clue. When we unplugged the front RCA connections from the HU, we could STILL hear music and noise through the front speakers, even though they didn't have a signal. When both the RCA's (front and rear) were unplugged from the HU, but the sub still plugged in, there was still a ton of noise, but no sound.

So my feeling now is that there is something wrong with my Focal 4.75 that is causing the noise to be radiated inside the amp. The sound from the rear speakers is also incredibly weak even when cranked, so something is wrong. More updates when I know more!

 

Is there a difference in grounding the RCA's at the head unit or at the amp(Asthetics aside)?

 

qhat is the gain at

 

Nope, no difference.

Gains are tuned properly, according to methodman, and I trust his call on that one. As for exact values, I'm not sure.

 

mark where there are ,then set the gains right down ........hay just try it

 

I'll give it a shot. Focal has said that they're going to give me a new one too.