I installed an aftermarket stereo system in April of 2007. About August of that year I started to get this whining from the alternator. It seemed at first to only whine in wet weather or when it got wet from an undercarriage wash, but then it just keep whining and seemed to do it more on hot days. New belt, electrical system OK, whine was still there. More than one mechanic said it was from inside the alternator and I'd just have to deal with it or replace it. I dealt with it, then finally, about 3 months ago, the original factory battery went dead and I jumped it and headed to the parts store and installed a new one. The whine magically disappeared, for good. I even drove through the car wash with the undercarriage wash and no noise. Two days ago a deer ran out in front of me and I slammed on my brakes and my subbox with the two amps connected to it got knocked around my truck and my remote amp wires were pulled out and many others were loosened, so I decided to redo all the connections. I of course disconnected the - of the battery and redid everything exactly as it was before. I started my car and the stereo came alive and I redid all my sound settings, I went for a short drive after and thought I heard some radio noise like when someone puts speaker and power wires together and you get that rpm sound when you accelerate. I turned off the stereo and the whine was back! The same exact alternator noise as before. Anyone know what this is about? I'm guessing because I unhooked the negative to work on my system, it reset stuff or something electrical happened and triggered the alternator. I just don't know. Tomorrow I plan to disconnect and reconnect the negative again to see what that does. It just seems that the battery has something to do with this alternator noise. I put in a new one, the noise is gone, I disconnect it to work on my stereo, the noise is back. Any help would be appreciated.