line volume of phone (aux) won't have anything to do with what your FM sounds like. You've either got a bad head unit or bad wiring. we need to find out which ...
PS... your iPhone, iPod, Android, etc... whatever you plug into that Aux port should have it's EQ settings flat. Let the head unit's bass and treble do the work..
My phone is low end and has no equalizer settings. I plan on picking up some speaker wire and pulling the fairing over the weekend and testing as you suggest. Do you know if the headunit is clearly marked as to which leads are the rears? In regards to the line volume, I know it does not effect the fm, but the the fm although it does break up is not nearly as bad as the aux is.