Here would be the method I would use,
Instead of a plywood box for large items, I use either plexiglass or acetate sheet. Simple to cut and bond together. It also offers a smooth surface for demolding. I will assume this to be a flat bottom hull. If not, you will need to build a support base of modeling clay for the hull that can be removed later. Afix the hull to flat smooth base with modeling clay. I like to make a 1/16 clay rope and put it at the bottom edge of the master and press it down to the base. This seals the master and holds it in place.
Normally, you only need 1/2 inch of rubber around your master, but 13x3 should get 1 inch to keep the walls from deforming. Cut two side sheets 2 inches longer and 1 inch higher that your master. cut two end sheets the same height of your sides and 2 inches wider. glue two 1/2 inch wide strips to the end near the top and bottom so they overhang the sides of the ends. These will align the ends with the sides and provide points to use rubber bands from end to end to keep the fence together.
I like to make small clay cones or square stock on the base between the master and the fence. Later when the mold is flipped over and the clay cones are removed, these become registration marks. Add 1/16 clay rope to the entire bottom of the fence and push down onto the base. Pour your rubber to the top of the fence which will be the bottom of the mold. Let it fully cure, remove the rubber bands and flip the mold over to the new bottom. Remove all clay from the bottom of the hull and mold. Use three or four lengths of large straws and some clay to create fill tubes. Put your fence back on to the mold with the top edge 1 inch above the the previous rubber level and spray/brush mold release to keep the mold top from sticking and fill to the top of the fence with rubber. When cured, demold and cleanup.
When ready to pour, the registration cones will be a huge help in keeping everything aligned.