Trigger, sorry no one replied to your posts until now. I think you need to beef the transom skin up from the inside (this will happen while putting in a new transom core) and use some good "putty mix" for the edge on the outside and then lay some 3/4 ounce CSM to shape it and then some 6 or so ounce cloth to to make it smooth and not build it up too much. Putty mix is a mix of resin and cabosil and chopped fibers. - that lower edge needs some beef added. I'd wait to fill/shape the lower edge until you have the transom in.
For the "dam", I'd use a sheet of melamine and screw from the outside into the 2" lip. If you look at the rebuilds section there are a lot of examples (my rebuild too) of doing this.
I decided to cut out the liner then finished removing all the foam.
Looking at the pic below - first off - nice work and the stringers look to be in great shape.
My concern is that you have not locked in the shape of the transom area = see the strap drooping? Do you still have the piece you cut out of the transom? If so, add it back long enough to get the structure right and then add blocks to the side of the hull, at the cap, and then lay a 2x2 or 4 across and screw into the blocks. You must lock this shape or you're creating a new hull. Oh - btw that is a killer storm you're looking at - where are you located?