amp noise, sub pop

Hopefully I can get some good feedback not only to help me, but others who may experience the same problem. First let me outline the install. 2006 Colorado Crew Cab Kenwood DNX7100 In Dash 2x Alpine Type-R components (front and rear doors) 2x Rockford Fosgate P500-2 2 Channel Amplifiers (powering the door speakers) 3x Pioneer Premier TS-SW1041D in a custom fiberglass box 1x Rockford Fosgate P1000-BD Mono Block The amps are mounted along the back wall with the signal cables run down the passenger side of the vehicle. The Power and Remote turn on are run on the Driver side. The whole thing is powered off of a 0 gauge wire off the battery to a distribution block and from there to 4 gauge wire out to the amps. Same deal with the ground, 4 ga. out of the amps into a distribution block, then grounded under the seat belt bolt on the passenger side. My problem: When the volume is turned all the way down on the head unit, I get the faintest whining sound, and it does react in tune with the alternator. Also, the vehicle is drive by wire, so when i tap the gas, I get a faint popping through the tweeters. The problem is not noticeable with the volume up, but knowing that it is there is mildly irritating. my other issue is, whenever i change cd tracks or radio stations, I get this thump from the subs. They sound fine when they are playing but like i said change a track "whump" and its not super loud, but noticeable. Any thoughts on where to even begin with addressing these issues. I have tried ground loop isolators and that didn't do it. Any help would be greatly appreciated, plus i know im probably not the only person with this issue

the head unit is run to a chassis ground., im going to scope out that sticky, thanks for the heads up