Ok guys, I found out what the problem was. One of my RCA's was bad and I had a reputable installer tell me I should wire my front door speakers directly to the amp. So, I re-wired the doors and changed the bad RCA. Re-ran both sets of wires right down the middle to the amp. And now I do not have any issues at all. My alternator noise is gone, my interior speakers all work and my sub kicks ass!! All is well, thanks for everyone that helped!
Syberman