I know pioneer head units have an internal fuse that is on the ground for the RCA's and a lot of times it is blown due to issues during installation. I know this is true for the RCA's but I don't know, if it was blown, and you were running on the head unit, if it would ruin the ground on the internal amplifiers input. May be worth separately grounding your RCA cables as well. Its obviously a ground issue, hence you were describing alternator whine (the higher pitch when you accelerate) tone. Gotta check your grounds! and take a look at the solution I presented.
