Well if you had static running your door speaker directly off your amp I think we can rule out the harness and the bose amp. Just for grins what kind of door speakers do you have?? And you are running rca directly from your HU to the amp. No funky connets adapters. Starting to sound like it's your HU. Not putting out a clean signal. I don't know.it if you had static in your 6×9 but those are not going through you bose. You have static in your whole system but your speakers are getting juice from different sources(bose amp,aftermarket) the only common source is the HU. I am no expert though. And it's static not alternator whine. If it was whine I would say your HU is not properly grounded. I guess it could be a harness?? Not your speaker part of it but maybe ground power remote etc. Could be picking up noise somewhere. But I'm just throwing darts in the dark.