Well folks I finally got my old Pioneer P-5200 HU installed. The previous problem I had with intermittent power was due to a loose wire connector in the Metra harness. (Bloody took me forever to notice the wire being pushed back out).

System desc.:

Pioneer P-5200 HU -> Scosche SLC-4 Speaker Level Convertor -> Metra Harness -> OEM Amp -> Speakers

* The HU and Level Convertor are both grounded using the factory ground wire.

However now I have a new problem for audio intelligentsia among us. I am not sure if this is alternator noise and it only happens when I play CDs. If I insert a CD I can hear faint clicks and the motor spinning up. I also hear a faint noise if the CD is playing with the volume turned all the way down. This does not appear to happen with the radio and the pitch and tone does not seem to vary with car speed.

My first guess was that I had set the gain too high. I tried turning the gain lower and higher but it does not seem to affect the noise.

I looking for a more educated opinion before I go tearing everything up. Everything I have found in rec.audio.car refers to noise in cd/radio or radio only, nothing in CD only. I'd appreciate it if someone could point me in the right direction. Thanks.

Have you tested for this noise with the car turned off?

If it only happens with the engine running, it is likely interference with the electrical system.

If it happens when the engine is off, then the issue is more likely related to the component itself.

It happens regardless of whether the engine is running or not? If it is component related what are my options? It isn't so bad that I'll lose any sleep over it. It just sucks to put in the work only to find out something isn't kosher. Thanks.

Finally resolved this silly problem. Beware: the following account includes acts of stupidity on par with driving while the hand brake is engaged.

After tearing up the wiring behind the headunit, I noticed the problem only occurred when I plugged in my subwoofer connection. Additionally, the sub output was kind of weak but I thought I just needed to mess with the headunit's settings. I never thought my cheap connection was the cause of my noise problem.

This connection consisted of a cheap RCA wire I had lying around. You know the kind you get with your VCR and stuff. I spliced this POS 24+ gauge RCA wire using butt splice connectors. I made a new wire using decent Scosche 18 gauge wire twisted fairly tightly and soldered it to a decent Neutrik RCA plug. I also redid my other speaker leads from the wire harness as I did not twist them before. (I didn't think such shorts lengths would matter).

Problem solved. I no longer have weird noise when the CD spins up and the subwoofer thumps much better now. I guess the old wire just wasn't providing a good signal to the factory amp. Everything just sounds cleaner.

So the lesson of the day is NOT to skimp on RCA wire and plugs. :) Especially since you can make better cables for cheaper than the high priced brand name stuff!