rca's popping when plugging in?

Hi guys, here is my set up and situation.

2007 Ford Expedition, Pioneer AVIC-D1 Head unit, Polk Momo C500.1 and C400.4 amplifiers.

3-12" Polk Momo Subs in a enclosure and 4 Boston Acoustic 5X7 coaxials in the doors. Now my problem.

Everything was working fine and no engine/static noise whatsoever.......until I decided to clean up the wiring in the rear cargo area where the amps are located. All I did was wire loom all the wiring to keep it looking nice and neat. Only wires I took off from the amplifiers was the grounds, power leads and RCA's from the bass amp (C500.1) Put everything back together and now when I start my truck up it has a lot of static in the coaxial speakers and loud! I read a lot of the issues here on the site and still no luck.

Both front and rear speakers have the noise, bass was left unplugged as it did not seem to effect it. Now I might have "stretched" the bass RCA's a bit to get them into the amp? What I tried next was removed power and ground from the bass amp and had the truck running and stereo on, took the RCA's from the bass amp and went to plug them into the amp with no power and I got a loud popping noise when doing so? Seems like there is still power to this RCA and it is loud when plugging into my amp? So..........help me out here fellows, should I try an new RCA lead from the deck to the bass amp? maybe thinking I tweeked the RCA's for the bass amp?

I did not touch the RCA's or speaker wires going to the C400.4 as there was a lot of extra wire left so I did not have to remove them from the amp. C400.4 wires were zip tied together so I just cutt them off and added the wire loom, now I got NOISE! Thanks in advance for your help or suggestions...........

Roger 

You've described the perfect way to destroy the ground plane inside Pioneer head units.  Where is that link "i am an idiot" posts all the time?

When you remove the ground wire from some amplifiers, the amp tries to find ground through the RCA cables that are connected to the radio.  Pioneer decided to protect their radios from amps that could have a shorted transformer and inject Positive or negative 12 to 80 volts to the shields of the RCA jack.  They protect their radio with a 3 amp fuse.  The Ironic part of the whole thing is, I have been doing this for nearly 30 years, I can count on one hand the number of amps that have the transformer shorted in a manner that the fuse would have protected the radio.   However, I can not count the number of radios I have seen with the fuse blown. 

Did you think he was calling you an idiot...I could see how his name in a sentence could seem very OFF...LOL