OK, I have had this plan for several years now, just never got around to it.
Take the top off, put it upside down in the garage with some lumber around the drip rail to support it. Get some A-B foam (not sure about the density) and fill the roof. Use a belt sander to carve down the high spots. Do a quick fiberglass cover to finish it off. Fast paint job and a rigid insulated roof. I could carve a little deeper where the cage is at, and maybe a Gurney bubble if headroom became an issue. Problems I thought of were the bolts at the windshield, I would weld them in from the top first, making them studs. I would also never be able to reach the bolts for the rear hatch afterword either. Neither a problem I could see. It would add a little weight to the roof, but I don't think enough to really worry about. Also it would be easy to bury a couple of wires in the foam for dome lights, etc.
I now have the spare hard top. I have finished the move into the new house. Just need that belt sander and some foam. Oh, and the time to do it.