I do not know what a used Hobie sells for in your area... from my experience here in TX parting out and finding a replacement would be the way to go.
If you decide to repair... I would try to remove the deck in one piece. Make the repairs to hull and deck separately. This will be still pretty difficult since in most areas you will deal with a sandwich made from composite material and a layer of foam. At least you will have space to work on the part from both sides. You will also be able to use a power sander to prep areas that would be otherwise not accessible. I would not try to make a mold and recreate the deck as a whole (to difficult for most people to build such a piece as a sandwich composite construction). Once deck and hull have been repaired just epoxy them back together. You could use a longer piece of stainless steel to create an anker for the shroud to spread the load over a larger area. Good luck.

Patrick