i dunno on here... i know a little about stereos and systems and whatnot...but you gotta be picking up the noise in the signal wire and that amplifier wiring...sounds like youre creating some sort of magnetic fields or something in the car. dont quote me on it or not (pick up a copy of the Car stereo cookbook by Mark Rumreich ISBN: 0070580839, or the newer edition) but that explains a lot about noise in stereos. anyway i think you should try and simplify your stereo wiring, it sounds like youve over complicated your power/ground distribution.. in my particular case im running a SONY XM-2200GTX hooked to a pair of type R DVC 12" alpines., with another 500 watt sony xplod amp for the components.. but i have it all run off of 2awg wire off the battery to a distribution block in the trim panel by the driver rear speaker..from there it splits into 4awg wire and a 8awg wire for the two amps...which reside in the trunk, with the grounds attached in the trunk also. I then run the signal wires down the passenger side to the rear. that way i kept all the wires as far apart from each other and the amps and grounds as far away from the alternator as possible. but if i were you, id see if i can simplify the wiring as much as possible and see if that helps...it may not but at least if you do theres less wires to have to chase around... :shrug ill do some reading and see what i can find out about eliminating alternator noise.. but i highly doubt its anything wrong with your alternator, i think it has more to do with where your stereo wires are ran. they may be close to a factory ground or something.