I have a 1982 R100 with a Enduralast EDL 450 alternator which makes what I would consider a normal whine except at exactly 3,000 rpm when it howles. The noise is not from the timing chain or nose bearing as they have all been replaced with no change. There's no run out on the rotor and the air gap is equal all the way around. The battery is good and all the connections are soldered.
It has done this as long as I've owned the bike, almost 7 years. The only reason I'm asking now is that I recently listened to one that was not as noisy.