it might be the harness. I know you said you checked everything but its the only explanation. If that harness has a exposed or loose wire somewhere than of course it going to do it to whatever unit you hook it up to.
just undo everything and redo the wiring. Take all of the speaker wires loose and try them one at a time and see if any of them play.
I'm lost now but this is what i would do to troubleshoot.
Pioneer has always been good to me. Alpine is one that has sucked balls in the past. So far only one has been good. And thats in the wife's car. she hasnt gotten past her radio station so that bitch doesnt get used at all.