Two points Jeff
1. I have been told by some fellows who buy and sell used boats as a past time/hobby/buisness that what guys would do to sell a boat that had a soft floor was to shoot some expanding foam into the cavities and let it set up.
Also I have been told that sometimes when a manufacturer put the foam into the fuel tank area to foam it in that it would also flow into other areas under the floor.
2. That stringer cut at an angle is not correct but sloppy workmanship on WellCrafts part. That should have been cut making contact at the right angle and epoxied in, then glassed in. Also if you go with a full transom, Good Idea then do as WellCraft did and add knee's that come up the transom about 14" from my memory. If that wood in that stringer is in good shape cut it back at an angle and make a scarf joint using one piece cut to be the right length to give you your knee also. Epoxy it in place and then glass it in. Guys like Skools can give you more details and have more experience than I will ever have but if I ever rip out my floor and transom to do that much work you can d@mn betcha that it will be stronger than what Wellcraft ever did there and done right.