01 - Preheat your oven to 350°F. Lightly grease a 9 x 13-inch baking dish with butter or cooking spray.
02 - Cook the jumbo pasta shells in salted boiling water according to package directions until al dente. Drain and rinse under cold water to stop cooking. Set aside.
03 - In a large bowl, combine shrimp, crab, ricotta, cream cheese, Parmesan, egg, parsley, chives, garlic, salt, pepper, and red pepper flakes. Mix until well combined and creamy.
04 - Melt butter in a saucepan over medium heat. Whisk in flour and cook for 1 minute, stirring constantly to form a roux.
05 - Slowly whisk in milk and heavy cream until smooth. Bring to a gentle simmer, stirring frequently, until thickened about 3–4 minutes. Stir in Parmesan, lemon zest, lemon juice, nutmeg, salt, and pepper. Remove from heat.
06 - Spread ⅓ of the sauce over the bottom of the prepared baking dish. Fill each pasta shell with the seafood mixture, about 2 tablespoons per shell, and arrange stuffed shells open side up in the dish.
07 - Pour remaining sauce evenly over the shells. Sprinkle with mozzarella and Parmesan cheeses.
08 - Cover with aluminum foil and bake for 25 minutes until heated through.
09 - Remove foil and bake an additional 10 minutes, or until bubbly and golden brown on top.
10 - Let stand for 5 minutes before serving. Garnish with extra parsley if desired.