Firstly, noise appears to come from my GPS box. ie, It disappears when I unplug it from the serial cable.

Okay, try powering it from the 12v permanent feed and/or the 12v ignition feed instead of powering it from the amp remote line. Second, try grounding it with a proper ground instead of the serial wire's ground.

In other words, your current setup has it getting both its power and its ground from the empeg. Doing the above will change it so that it gets its power and ground from the car instead of the empeg.

EMI being picked up on the outputs. Grounding the barrels of the RCA adapter reduces it. Any barrel, F/R, L/R, helps. I'm guessing that if I gave all 4 a good grounding this noise would be eliminated.

Grounding one is probably going to be the same as grounding them all, I'd guess.