Just my observations: As far as the water goes, I've never seen a leak through the hull that fills to a certain level, and then stops. What would make sense to me is backflow from the bilge pump hoses. The pumps can't evacuate all of the water, and some of it inevitable flows back down into the boat.
The trunk underneath the door looks a little off-kilter, and my intuition about the mystery screw heads along the centerboard trunk in pictures 4 and 5 was that somebody bolted a metal reinforcing plate to the back side of the liner to shore it up. Picture 1 seems to show a metal plate bolted to the inside of the fiberglass liner, in exactly that location. Is there any cracking or deformation of the overhead and deck which suggests that the compression post has sunk beneath the mast? (It does not appear so in the pictures.) I can't imagine how anybody could maneuver the plate into position, except during construction of the boat, so it seems it was built that way.
I have a 1974 boat, and the ballast looks very different. It, and the centerboard trunk, are completely encased in a single, monolithic block of lead and resin, bonded to the hull. There's no path for water to flow fore and aft, except over the flat top of the whole ballast/trunk.