Jason, this is the same thread I followed when I added a starboard battery box prior to this season on my 2002 SAN. I have two flooded group 27's under the starboard seat in the back and kept the single starting battery on the port side--didn't have any problems this season.
Just make sure to fill the cratered areas back in with foam so that it's as straight as possible, then glass over it with a couple layers to add strength/rigidity. Most likely, with the added support from the fiberglass box, it will be stronger than it was from the factory.
Also, if you're looking to enlarge the port side box, check out this DIY--Eric did a nice job on it.
http://www.planetnautique.com/vb3/sh...ox-enlargement