Splash Well cutting ?
 

Wondering what the best way to cut the splash well up to make it easier to repair my transom and stringers? any ideas ?

No real easy way just start cutting!! Just make sure you cut were it is easy to re glass it back together.

For the amount of work you are planning to get into, think about the project as a whole.
You are toying with mounting the batteries up front, you may want a sleeve (pvc pipe) for the wires to go to that location beneath the floor instead of hanging them with the rest of the wires and steering, that cable will be awfully heavy.
While cutting the floor and back splash to access the stringers you might want to look at the possibility of modifying for a bench seat, keeping in mind about regular access to the bilge pump(s) and drain plug. Also look at the permanent fuel tanks that may be hidden in that location if replacing the saddle tanks become an issue.
Here are some for standard dimensions.
http://www.moellermarine.com/afterma...rmanent_tanks/
reelapeelin has his tanks in the seat boxes. If you rather have that setup, add a sleeve at those locations also.

And PLEASE take pictures as you do whatever you do.