My 1999 Contour SE Sport 2.5L ATX did the same thing, the speakers whistled, and it got worse the faster I went, or if I turned on the air. I did not have an aftermarket HU or speakers. Turns out that when I took the car in because it wouldn't start, the dealer found a lose ground under the dash, and when they tightned it up my whistling went away. Even if you didn't take apart your dash, look for a lose ground anywhere near you HU, speakers or Amp, cause a loose ground can cause interference. My car's wire was lose because the dealer forgot to tighten it after a service. However I found another wire in the trunk that was a little loose, and the dealer never did any work there. So like I said check the grounds.