Thanks guys. I used a Dremmel type tool and I seriously don't think I would have been able to do it without it. Some of the wood was a bastard to get out, but I was able to get it out piece by piece with the multi tool.
So far, both sides are cut out and sanded and I've cut and dry fit the new plywood. I used the old fiberglass skin as a template.
I taped off and covered the aft gunnels and deck with a painter's tarp as the next part of this project will get a little messy. A friend suggested screwing the new boards in from above to hold them in place, so just I'll use the holes from the rod holders.