Sounds like an earthing problem to me, I had a similar whine and turned out to be just that. I fitted a JL amp under the passenger cubby (secret floor) wired straight to the battery and then followed the OEM wiring to the speakers, took longer to remove the interior than it did to do the wiring. Also then wired in a sub to the boot, again took longer to remove all the trim than to actually do the wiring.