If the boxes are built on top of the deck, meaning ... the deck is the floor or the bottom of these boxes, take an angle grinder with a cutting wheel on it and score the seam between the walls of these boxes and the deck. This will free the boxes so you can left them off the deck. Post some actual pictures of what you see as opposed to hand sketches so we see what you do.
If the wood core of the stringers is solid and dry, no need to replace it, Use the same cutting wheel and cut out the de laminated fiberglass (From the picture, this is the portion of the fiberglass that extended to the hull) be careful not to score the hull itself... grind the fiberglass that still has good bond with the wood to rough it up a little... clean with Acetone and use two or 3 layers of 1708 to reglass the stringers to the hull. Make sure the wood is not wet or moist. If so, just take it out and start over. You are very close right now, you don't want to save couple of days of work only to redo it over in few years
