try and ground everything to one spot and don't use the ground wire in the radio harness from the car, take the black wire on the radio, the ground you add to the rca and radio chassis and ground it all to one spot, i'm pretty sure the main culprit is radio ground wire attached to stock wire harness...

try soldering a ground wire to your rca cables at the back of the radio and then ground that to the chassis. i have a pioneer dvd nav unit that had the dreaded whine and it almost drove me crazy for a year, finally broke down and did this and also took the ground wire from the radio and grounded it ...