Grounding Issue
Are you running a high perf ignition system? I've read that these things can cause noise in a stereo as well.
Something else to try is to run the power (+12 constant, and +12V switched, GND, etc) off of another power source like another battery. Start the car up and see if you're still getting noise. If not, then the noise is being induced through the power/GND wires. If you're still getting noise, then it's being induced into the radio itself. In which case, I would try a different radio.
You could also try pulling the HU out while the car is running to see if the noise changes at all.
Did you have noise in the original system?
When I installed my aftermarket HU into the 97 z28, I used one of those adapter harnesses, used the factory +12V constant, +12switched, GND, and dimmer leads (amp'd system). I had no noise with the oem, nor do I have noise with the new stuff..
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