Preheat your oven to 375°F (190°C).
Boil the jumbo shells in salted water according to package directions until al dente; drain and set aside.
In a skillet, heat oil and brown the chicken sausage with the red bell pepper until cooked through.
In a bowl, whisk together pumpkin puree, milk, oregano, red pepper flakes, salt, and pepper; pour into a 9×13 inch baking dish.
In a separate mixing bowl, combine ricotta, 1 cup fontina, and the basil pesto until smooth.
Stuff each cooked shell generously with the cheese and pesto mixture.
Arrange the stuffed shells over the pumpkin sauce in the baking dish.
Top with remaining fontina and torn fresh mozzarella.
Bake for 20-25 minutes until the cheese is bubbling and slightly browned.
Serve warm, topped with fresh basil.