Good advice so far. I would epoxy one layer of biaxial on the old skin first and then with your core already pre made and ready next cabosil that to the still hot biaxial/cabosil on the old skin. Clamp that sucker in place so the cabosil gets squeezed out around the edges of core. I like 2x4's thru bolted into the transom then fillet all the voids around the core were it comes in contact with the hull. Let this all set up and then remove the clamps and start laying up the inside. I would use use biaxial and make the inner glass approx 1/4-3/8 inch thick. As far as how to work with large pieces of glass I usually cut it so it will drape over the transom and kinda hold itself up. Anyway you go about it it's still gonna be messy. I like to use OB sleeve (fingerless) with 2 latex gloves over my hands as that will keep the epoxy off your arms.
strick