Plug something with an RCA output, like a portable CD/DVD player or Ipod into the amplifier's inputs and see if the amp is actually working properly or not.
Plugged my portable dvd player into the amp and sure enough the subs hit. So what does that mean, it has to be something with my RCA's? Right? I took both the wiring harnesses out and re-did all the connections. I'm stumped...
Try plugging that DVD player into the amp THROUGH the RCA cable (on the D3 side of the cable) so you can discern whether it's the unit or the RCA cable that's not working right.
Also, check to make sure that you inserted the mute wire pin in the correct position and that you haven't accidentally disconnected any of the necessary RCA cable connectors from the wiring harness.
And just to be 100% sure here, you did relocate the pin position of the mute wire when you grounded it as per the bypass instructions, right? Because if you ground that wire while it's in it's original position, it will mute the radio.