Thanks for the wiring diagram, that's VERY helpful.

Just for the heck of it, try these two things:

1. Remove the capacitor and see if the noise disappears.

2. Try sending the rear RCA's straight to the infinity subwoofer, and the front RCA's straight to one pair of channels on the four channel amp.

If that second thing gets rid of the noise, you can use the amp's front passthrough, chain it to the rears, and have the front fader be the regular speakers and the rear fader be the subwoofer level. Adjust the front/rear fading of the regular speakers by adjusting the amp gains.