travisroy
+1y
Start by unhooking the RCA's from the amps input, does the alternator whine remain? If so, then the problem is probably in the amp and /or its power wiring.
If the sound goes away, then plug the wires back in to the amp and disconnect the other end from the back of the head unit. If the sound remains this time then try running the RCA cables from the head to the amp outside the car and see if it is there. This way you can tell if its the RCA cables that are picking up noise or if its the location of the RCA's that are injecting noise into the signal. If its the location, you can reroute the cables problem solved. If the noise goes away when you removed the RCA's from the back of the headunit, then the noise is coming in via the headunit and/or its wiring.
If its the headunit, then try temporarily running a wire from the ground of the head unit to the ground of the amp, if the sound goes away at that time then you should be able to reground the head unit to a better location (some people would even run a ground to the amp's ground permanently but I dont believe this is necessary).
Hope this helps.