01 - Preheat oven to 350°F. Lightly grease a 9 x 13-inch baking dish.
02 - Cook 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.
04 - Melt butter in a saucepan over medium heat. Whisk in flour and cook for 1 minute. Slowly whisk in milk and heavy cream until smooth. Bring to a gentle simmer, stirring frequently, until thickened (about 3–4 minutes).
05 - 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.
07 - Fill each pasta shell with the seafood mixture (about 2 tablespoons per shell) and arrange stuffed shells, open side up, in the dish.
08 - Pour remaining sauce evenly over the shells. Sprinkle with mozzarella and Parmesan.
09 - Cover with foil and bake for 25 minutes.
10 - Remove foil and bake an additional 10 minutes, or until bubbly and golden.
11 - Let stand for 5 minutes before serving. Garnish with extra parsley if desired.