Well for the holes on the back of the boat , this is an idea there are probably alot of ways to do it but this is one. You could use something like this
http://www.grainger.com/Grainger/items/3LN64 and silicon around or epoxy in so they will be water proof. They start at 1/2" and go upto like 2". I was thinking easy fix without having to do painting or more complicated patching, and they don't look that bad.
Paul