Richard,
My fuse bottom looked much like yours before I went to work on it with a razor plane and sanding block. Yes the fuse sides were higher than the hatches. The key is to form them to follow the shapes defined by the fire wall, F2 and F3. Just sand them to make a smooth transition from one bulkhead to the next. After sanding to final shape, I used strips of 1/64 ply to line the inside edge of the fuse sides. This will support the soft balsa sides where they come to a point. You will of course need to sand the width of the hatches to allow for the '64th ply. I added two 1/8th dowels to the fuel tank compartment hatch with corresponding holes in the fire wall. Then I added a small ply faced block of balsa to rear of that hatch so a 3/16 dowel from the front of the back hatch going through F2 will lock it in place. The back hatch has two magnets at it's rear to hold it in place.