'03 Accord - Alternator Whine

I have used the Audio 2000 trouble shooting guide to narrow down the source of the noise as coming from the Factory HU speaker outputs. The amp and the signal cables all test clean. I am using a Navone Engineering N-774V four channel line out converter connected to an ads P440 amp. When I disconnect the antenna the noise is significantly reduced to an acceptable level. How can I reconnect the antenna without re-introducing the noise? I've heard of ground loop isolators but I'm not sure you can use these on antennas.
One last thing. It would be nice to eliminate every last trace of noise and I suspect it may be coming from the ground suplied by one of the wires in the vehicle harness, or perhaps the power wire. Does anyone know where I can get a schematic or something that will show me the color codes for the wires going to the factory HU?
 
Update:
Ok, so it's looks like no one had any suggestions. Well, I was about to install an antenna noise reducer when I realized I had routed the power wire for the amp along the antenna wire. After re-routing the power wire the antenna is no longer introducing noise into the system. But I still have very a slight amount of alternator whine left. I know it's comming from the factory deck, so I guess I will now try attaching a noise reducer to the power input of the factory deck.
 
Assuming you are refering to the power supply for the Amp:

Power - Aprox 12 ft of 8 AWG cable connected directly to the positive terminal of the battery, routed down the center console and under the rear seat to the trunk.

Ground - Less then 12 inches long and connected the chasis. Bare metal contact acheived by grinding off the paint.

As mentioned above, I have gone through extensive trouble shooting to narrow the source to the factory deck. The signal wires and the amp are clean. Although, I'm still left wondering why the factory deck had no alternator whine before connecting the Amp.
 
Sorry 'bout the delay;

I assume you have power feed noise filtering near the amp's power input lead. If not you should try an inductor / capacitor filter near the amp. I have generally made my own as many commercial products I tried were unsatisfactory.

I would also try running a seperate ground lead from the chassis ground back to the battery terminal.

Another idea (worked for me once) is a ground wire attached to the amp's chassis and run back to the battery terminal. The amp's chassis is then isolated electrically from the car.

Sorry if I have told you to suck eggs you may have done all of this already.

Cheers
 
The remainder of the alternator whine is now gone. I have 4 channels of RCA cables (2 pair) running from the LOC back to the amp. The RCA cables run perpendicular to the power cable and are only 6 inches away. I have one high-end pair of RCA's and one mediocre pair, apparently. So, I switched the high-end pair and the mediocre pair from the sub to the high/mid section, respectively, and now the system is virtually noise free.
thanks for all the helpful advise.