I'm only slightly ahead of you on my first boat restoration project so please take this for what it's worth. I used a circular saw for making cuts to my transom since I could set the depth of the blade. There are other tools that may work better since a circular saw can be cumbersome, dangerous when cutting upside down and hard to reach the interior corners for certain cuts. May not be a problem since you are attacking from the outside.
As for the epoxy I've gone with the West System but if you read the site very much you will see a lot of debate over what people prefer. When doing my homework I went to their website for application techniques, etc.
http://www.westsystem.com/ss/use-guides/
Good Luck!