Steve,
My thoughts are if you are running open road it's a bad connection from stator plug or the Regulator or a bad cell in the battery. If you can get the battery load tested that will help pinpoint your issue. Good luck, let us know how you are doing.
Yamaha replaced that with an isimple that comes with an ipod touch for about that price and you still have your whole bag. We ran the chord out use the iphone plugged in for tunes and gps and that works great.