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Sounds like you should try twisted pair RCA's...
From some guy on some audio forum...
"Engine noise" is really alternator noise. The alternator in your vehicle cranks out AC electricity, and the rectifier on it changes the AC to DC electricity that can be stored by the battery.The rest state of the battery is lower than the output of the alternator, but since the alternator isn't constant in its output, but rises and falls, there is an AC quality to the voltage state.
This usually doesn't hurt anything. But unfortunately, since Edison abandoned the completely mechanical gramophone that worked with a toothpick and a horn, audio systems have used low-level AC to "mimic" the air pressure changes that we hear as sound.
The low-level AC signal goes into an amplifier and gets made into a high-level AC signal strong enough to push a speaker in and out (using the speaker's magnet as a fulcrum - but I digress). But before it gets there, in certain conditions, the AC floating around your car's electrical system can get added to the AC signal heading for your amp. This is why, when you place a greater load on your alternator by turning on your lights, cig lighter, or rear-window defogger, your noise gets louder.
And that's "engine noise". (And you now know more than everyone at Circuit City, but regardless...: )
There are really three kinds of engine noise:
1) The kind that is created inside the component due to poor power input filtering. The AC coming in the unit's power wires somehow ends up on the audio output. This is usually bad design. This is rare, and don't assume bad design, cause it's usually bad installation. This can usually be addressed by filters on the power wire. This is only the case nowadays with crappy gear. BTW - if the head unit diodn't have noise before, and it has noise after you add an amp, you can pretty much tell that this isn't the problem. If you have a signal processor (Xover, EQ, etc.) sometimes they need more filtering.
2) The kind that is picked up by your RCA or signal cables between two components. This is called inducted noise. (Technically, you an get inducted noise on your speakers too, if you place one of your speaker crossovers next to a power wire and the coil of wire in the crossover is next to the wire and acts like a super-long antenna, but that's pretty rare.) This is fairly common in Honda-based vehicles, and all the kinds of "shielded" RCA's never helped one car I ever saw. However, twisted-pair signal cable works great! I can't tell you how many cars had their noise eliminated with this simple addition. It's all I use now - even the entry-level twisted is better for car use than the most expensive straight-conductor RCA's.
3) Ground loops. I will not even try hard to explain ground loops (they basically mean that there is a difference in how easy it is for electrons to loop back to the battery - for one of your components, fewer electrons can make the trip. The electrons look for a way to get home - back to the battery, that is - and they end up making the trip on some audio signal cables somewhere. There, that's all you get - if it didn't make sense, too bad : ) Here is how you go about getting rid of them:
Ground all components to the same point, with no paint under the connection, and under a bolt rather than a screw if possible. Bad grounds are the single biggest cause of engine noise.
Make sure your battery is in good shape. Weak and low batteries fail to do their job of buffering like they should.
Try RCA's that are only grounded at one end. (Hey, it might work...) Also, if you have a signal processor, try lifting the ground for it and see if it makes a difference.
Try a ground-loop isolator. Most of these make your system sound worse, especially in bass response. They often get the noise out though. I usually use them for troubleshooting more than for installations (the one in my tool box has been there for years).