When you refit the cover, be sure to protect the metal from corrosion due to dissimilar metals by using a dielectric paint on the steel bolt threads (such as duralac or starbrite) before screwing the bolts back into the engine block for the alternator cover. Do a search on starbrite and you'll probably find an old thread on the subject.
If your bike has a sound-deadening sponge beneath the alternator belt cover, throw it in the bin as it retains salty water from the roads.I would paint or spray some ACF-50 under the alternator belt cover to keep corrosion from starting.
I would also strongly advocate fitting one of Mark Hootons crud catchers to the front of the engine to prevent it getting stone chipped or blasted by grit from the front tyre.