Since you're going to remove the cap, I would do a complete restoration; transom, floor stringers etc. The transom: once the floor is removed cut around the perimeter with a cutoff wheel on a grinder. All you're doing is putting a score line around the transom to remove it, so you don't need to cut deep. Second you'll want to make some wooden wedges to drive between the outer skin and transom, that should break it loose. Be careful not to damage the outer skin when doing that. Try to remove the transom in one piece to use for a pattern. Attached is a visual of how to install the stringers,floor and transom.
Edit: You'll need to build some transom clamps when you're ready to install the transom. Here's the link:http://checkmate-boats.com/forums/showthread.php?t=23591
For core repair:http://checkmate-boats.com/forums/showthread.php?t=27838
Edit: You'll need to build some transom clamps when you're ready to install the transom. Here's the link:http://checkmate-boats.com/forums/showthread.php?t=23591
For core repair:http://checkmate-boats.com/forums/showthread.php?t=27838