After posting a photo of my rubbing alternator belt and the broken alternator bolt on the Beta Marine forum, someone pointed out that I was missing a spacer at the bottom of my alternator. A few calls at lunch to the Beta Marine distributor at lunch verified that it was a standard Kubota part. A quick call to the Kubota dealer verified that they had four in stock.
This stupid spacer has been the cause of all my headaches. In fact, I think I remember seeing one of these rolling around the garage at some point, but I didn't know what it was or where it went, so I think I threw it in with all the bolts and pieces I crated up with the old Kubota block I sold.
Hopefully this is a $5 miracle fix. Unfortunately we have to wait until after the trip to Florida to find out.