The red circles are call knee braces, this is what Skeeter refers to as their Kneed Transom. Removal of the top cap is straight foward, except with bass boats you have some extra issues. Mostly the plumbing for the livewells need to be disconnected, the biggest issue is actually freeing of the cap. Not sure what model you have but Skeeter shot flotation foam everywhere on mine, if the foam was touching the deck when it setup then it stuck to it. Mine is stuck under the seats, which is not a big issue you just have to do some prying and scrapping. A long thin metal tool will work best. Most boats are permantly attached at the juction of hull and cap in the transom area. Bass boats pose a new problem you cant easily get from the bottom to cut through the resin they use. A few options exist, work hard from the underside with "custom" made tools, apply upward pressure and hope it will free itself or just cut it. The last to are going to result in repair after the fact, i personally have chosen to cut the very top skin, then to cut the pieces apart... Atleast with this way i control how much i need to repair or rebuild.
Judging from the last set of pictures i can assume that the stringers atleast are rotten, which as with most boats they rot from the bottom up and back to front. Transom is more than likely on its way to full rot, obviously the floor has started to go. Not sure on your year but Skeeter would use a balsa wood core in certain areas of the hull, if you choose to rebuild those areas will need to be cut out and replaced as well.
