Bring a large pot of salted water to a boil and cook the jumbo pasta shells until just al dente. Drain and set aside to cool slightly.

Heat the olive oil in a skillet over medium heat. Add the minced shallot and one minced garlic clove, then cook until softened. Stir in the fresh spinach and cook until wilted. Transfer the mixture to a bowl and let it cool.

Mix the cooled spinach with the ricotta cheese, 1/4 cup of the Parmesan, nutmeg, and a pinch of salt and pepper until evenly combined.

In the same skillet, add the remaining minced garlic and cook briefly. Stir in the pumpkin puree and heavy cream. Season with salt, pepper, and the remaining nutmeg. Simmer gently for a few minutes until the sauce thickens slightly.

Preheat the oven to 375°F. Spread a thin layer of pumpkin cream sauce in the bottom of a baking dish. Spoon the ricotta filling into each shell and arrange them in the dish.

Pour the remaining sauce over the stuffed shells and sprinkle with mozzarella and the rest of the Parmesan. Bake for 20 minutes until the cheese melts and the edges bubble.