Does the noise increase with the engine RPM? If so, you have alternator whine. This is due to a 'noisy' ground, bad ground, RCAs traveling next to a high current wire, or poor power filtering at the source or amps. Additionally, you shouldnt hear this noise coming from the subs since the filter in the amp blocks at that particular frequency due to the low pass filter. In the future, use twisted pair RCAs which are excellent at rejecting induced noise.
Or is the noise constant? If so, you have an RCA traveling past a computer. If so, find where the RCAs are traveling across a small metal box. The vehicle's computers are known to emit radio frequency which can be induced onto the RCAs. To verify if this is the case run sum long RCAs from the radio, outside the car into the trunk and see if the noise goes away.
My guess is that the difference in ground potential is the culprit. That means the resistance to ground at the source unit is different in comparison to the resistance to ground at the amplifier. Try moving the amp ground wire to another point in the vehicle to see if this changes the level of the noise. Likewise, try moving the source ground to another point to see if the noise decreases.
How old is the battery? The battery is the primary device to filter out AC ripple from the alternator. Older batteries are known to allow more AC ripple through to the system. And of course the only way to detect this is via an osciliscope or when you can hear the alternator whine. To check this just connect jumper cables to another (newer) car and power your audio system with their electrical system. Leave your engine OFF during this test.
Speed pulse will have to be found at the instrument cluster. You will need an electronic wiring diagram to find the correct wire to tap for the vehicle speed pulse (VSS).
Good luck!
