Preheat the oven to 375 degrees F. Cook the gluten free jumbo shells according to the package directions until just barely al dente. Drain, rinse gently with cool water, and lay them on a lightly oiled sheet pan to prevent sticking.
In a large bowl, combine the ricotta cheese, 1 cup of the mozzarella, parmesan cheese, egg, chopped spinach, garlic, nutmeg, salt, and black pepper. Stir until well mixed.
Spread 1 cup of marinara sauce evenly across the bottom of a 9x13-inch baking dish.
Spoon about 2 tablespoons of the ricotta filling into each cooked shell. Arrange the stuffed shells in a single layer in the baking dish, open side up.
Pour the remaining 2 cups of marinara sauce over the stuffed shells, making sure each one gets covered. Sprinkle the remaining 1/2 cup of mozzarella evenly on top.
Cover the dish tightly with aluminum foil and bake for 25 minutes. Remove the foil and bake for an additional 10 to 12 minutes until the cheese is melted and bubbly.
Let rest for 5 minutes, then garnish with fresh basil and serve.