I am thinking that this is not just a regulator problem. Rockhopper is right that there should be over 14V across the battery when charging, and on mine I think there is 11.7V when engine is off.
The other symptoms you describe seem to suggest there is something mechanical going on too. Was it only the STs that had alternator rotor nut problems? I do not know enough about the 916 series to comment.
A short in the alternator coils would also cause problems with the "back EMF" which would have a tendency to fight against the engine. Not sure how much that would be noticable and give you a feeling of "running like a bag of nails".
We're sure this is "bag of nails" is not normal Ducati clutch rattle? My ST2 was described as "dragging a shoping trolly down the street"!
