Bring a pot of salted water to a boil and cook the pasta to al dente, about 2-3 minutes shy of the time on the box. Reserve 1 1/2 cups pasta water. Drain, rinse with cold water, and set aside.
To make the filling: whisk the ricotta, egg, nutmeg, and parmesan together until smooth. Season with salt and pepper and fold in the mozzarella. Transfer to a piping bag or a large ziplock bag.
To stuff the shells, cut off the tip of the piping bag or the corner of the ziplock bag and pipe the filling into the cooled shells. Set aside.
Preheat the oven to 425 F. Melt the butter in an oven-safe skillet over medium heat. Once the butter is melted and foamy, add the sage leaves. Fry for 2 minutes per side, until darkened and crispy. Transfer the sage leaves to the paper towel-lined plate.
Add the shallots, garlic, and crushed red pepper to the skillet and cook for 2-3 minutes, stirring occasionally, until softened. Add the tomato paste and pumpkin puree and cook for 1 minute. Next, add the vodka, bring to a simmer, and cook for 1 minute. Add the pasta water, bring to a boil, and reduce by half. Pour the cream into the pan and bring to a simmer. Cook for 2-3 minutes, until thickened. Turn off the heat and gently arrange the stuffed shells in the sauce. Top with mozzarella and bake for 25 minutes. Broil for 2 minutes towards the end to brown the cheese.
Remove from the oven, top with the fried sage leaves, and serve.