I have owned this boat for 3 years and in those 3 years I am replacing the top alternator bracket for a second time. Was/is there a problem with this or should I look at the bushing on the bottom bracket?

What year is the engine. If its a 2004 or older with the bolt adjustment for the serpentine belt, you're tightening the serpentine adjustment to tight and most likely breaking the bracket. Follow Merc adjustment procedure called out in the service Manual. You could also have some other form of alignment issue on the serpentine system.
I am always amazed at how many 496 owners will invest so much money in a boat and not spend a tiny few dollars for a manual?!

Regards,
Ray @ Raylar

And Diagnostic software or scan tool.