No, it's not your fault about the confusion. I'm more puzzled about the amps. I'm thinking your amps must be bypassed simply because it doesn't make a differnece if your amps are plugged in, yet vibrating the plug changes the tones. Hmmmm. You would definitely notice the difference if the front door subs were not working. They thump pretty well under normal conditions, unless they rigged it somehow.
I looked around on Crutchfield, and the only harness that I found was for a basic radio set-up. You just plug it into the stock harness, and wire it to your radio. It would use the basic wiring structure, but not sure if it would go to your amps. The mach system uses low voltage signals to the amps, not typical wattage to speakers. Did you have alot of distortion when turning it up?