Noise issues in a brand new Fusion

Hey guys, let's see if you guys have any ideas to solve a noise issue in a vehicle.  I've tried everything I can think of.

Vehicle:  2006 Ford Fusion

Equipment:  Alpine CDA-9857 head unit with ipod cable attached and SWIX steering wheel controls installed;  Old school Kicker 4 channel amplifier (not sure what model) running Focal components all around;  Old School Phoenix Gold amplifier running Kicker Solobaric subwoofer.  The amps and subwoofer the customer brought in.

The customer left, then came back in the next day because he didn't like the looks of the head unit in the kit.  I was on another install, so the manager took the deck out to look at it, and when put back in the customer came right back in saying a noise all of a sudden showed up.

The noise was a constant hum along with alternator whine.  We tried running a reference ground from the amp to the head unit and the noise got worse.  Running a set of RCA's through the center of the car didn't help.  We then connected the RCA's I ran to the shop CD player, so the signal is running through my ran RCA's, and the noise completely went away.  That eliminated everything from the head unit back.  We tried swaping out the CD player, and that didn't help.  So we tried powering the head unit with our shop's power supply, and the noise was still there.  We even tried cutting the dimmer wire to see if it was coming through it, and that didn't help.

Putting noise filters on the RCA's did completely get rid of the noise.  However the customers saw us walking with them to his car and complained saying he didn't want any noise filters in his vehicle.  I should also mention that turning down the gains on the amplifier did reduce the noise volume, but didn't get rid of it completely. 

Anybody have any ideas?

i had the same problem doing a fusion about a month for like 2 weeks there was no noise then all of a sudden it showed up well i found that a little of the insulation on the rca's rubbed off so the so the rca's was pickin noise up from the metal frame cause its a ground try checking the rca's from front to back or jus completley start over and run all the rca's by them selfs with nothing around them at all if it still persists its gotta be the amp or the car cause i know mid 90's camry's are natorious for noise i hope that helps a little and i know u know more than i do so good luck

Dyohn:  I actualy tried that.  We have a test bench in our shop with a power supply and head unit.  It's where I got that external signal to run through my RCA's.  I also tried powering the Alpine head unit (power, ground, and accessory wires) with it and the noise was still there.  That's what made the problem so confusing. 

It's almost like it's a radiated noise being picked up by the head unit itself.  I guess I could see if it is there with the head unit out of the dash.  Sounds like a bit of Mu Metal for shielding might be in order.

Jayson, if it was the RCA's or amps, then the noise would have been there when I ran a signal from the shops head unit through those RCA's and into the amps.  Since it wasn't there, that means they aren't the source of the noise.

Rob reminded me, I also disconnected the antenna with no luck either.  The amps are mounted to MDF, and the power and RCA's are run on opposite sides of the vehicle.  I think you are right Dyohn.  I have eliminated every other possible source for the noise.  It has to be radiating directly into the head unit.