You may want to check the wires coming off of the alt. There is a connecter there that can over heat and cause a voltage drop, then get really hot, then cook electronics from low voltage. It has been an issue in the past on some bikes. Make sure that connection is clean, take it apart and inspect it, just looking at it doesn't cut it. When you get the replacement alt, take a voltage reading at that connector and another at the battery, with the engine running at 3-4k rpm, with low electric load, i.e. no extra lights or accessories. You should see the same voltage, or very, very close.