I have removed all the Bose speakers and deck and I have a sub amp and a amp for my rears and fronts. I have a good ground and ran the rca's and power on opposite sides. I have been trying to fight alternator whine since. It seems to be more noticeable when I have the lights and heat on. I think I have checked the basics. Any other things I am missing? Thanks.

 

Re-do your grounds. Make sure the main amp ground has good contact with the body. Make sure your antenna is securely attached at the headunit (this was the source of my horrific whine).