Electrical noise

Hello, so I have had an amplified system running in my car for around a year now with no issues. All the wiring is fine and all the grounds are firmly secured to the chasis. however a few weeks ago i started my car and noticed a whine coming through the speakers that changes with engine rpm. Since then I've noticed that when i have the key in the "RUN" position my speakers pick up noise from the fuel pump priming, and when i turn the headlights on it creates noise. I want to think that i have alternator whine but the alternator does not do anything when the car is not running. The noises vary with engine rpm but also anything that uses the cars electric system (headlights, charging a phone, interior dome light, etc). I've had all my grounds tested and all my connections tightened and tested and there is no issue there. One thing that i have noticed that i believe is odd is that my head unit runs fine without the ground wire attached and when I reconnect the ground wire nothing changes with the engine noise / electrical noise. the head unit seems to be grounding through the antenna because if the antenna is disconnected then the head unit will not turn on. if anyone has any ideas / suggestions it would be greatly appreciated. 

thank you