I'm not sure I understand what you are saying above. It sounds like you swapped out the amp and it worked, but you still think the problem might be with the HU. I don't understand the logic.
Regardless, if you have been swapping RCAs on in and out, you may have blown the pico fuses in the Pioneer HU - which breaks the RCA ground connection and will kill the RCA signal level. Try grounding the RCAs to the HU chassis like shown here. Look at the HU in the background, note how the wires attach to a chassis screw...