[strick]

I'd base my decision on the following: Ask yourself how long do I want to have this boat. If the answer is "for a long time" then I'd do what you originally had planned and put a bracket on it. It will take a long time to complete but will give you something to do over the winter months and you will be happy that you did what you wanted to do and it will look great when it's finished. If you go this route then I'd free up some of the space in the stern like you suggested by removing the fish boxes etc.
However if the answer to the question is "for a short time" then I'd assess the damage and do a quick fix to aleviate the problem. Sounds like you need to do a few test drills at various places on the transom to see how much is rotton or wet. It may not be as bad as you think espically if the transom has no flex. Hope this helps.

Strick