01 - Preheat oven to 350°F. Lightly grease a 9 x 13-inch baking dish with butter or cooking spray.
02 - Bring a large pot of salted water to boil. Cook jumbo pasta shells according to package directions until al dente. Drain and rinse under cold water to stop cooking process. Set aside.
03 - In a large mixing bowl, combine shrimp, crab, ricotta, cream cheese, Parmesan, egg, parsley, chives, garlic, salt, pepper, and red pepper flakes. Mix thoroughly until all ingredients are evenly incorporated. Set aside.
04 - Melt butter in a saucepan over medium heat. Whisk in flour and cook for 1 minute, stirring constantly to create a roux. Slowly whisk in milk and heavy cream until smooth and no lumps remain.
05 - Bring mixture to a gentle simmer, stirring frequently, until sauce thickens and coats the back of a spoon (about 3–4 minutes). Stir in Parmesan, lemon zest, lemon juice, nutmeg, salt, and pepper. Remove from heat.
06 - Spread one-third of the white sauce evenly over the bottom of the prepared baking dish.
07 - Fill each pasta shell with approximately 2 tablespoons of seafood mixture. Arrange stuffed shells in the baking dish, opening facing up, in a single layer.
08 - Pour remaining white sauce evenly over the stuffed shells. Sprinkle shredded mozzarella and additional Parmesan cheese across the top.
09 - Cover baking dish with aluminum foil. Bake for 25 minutes until heated through and sauce is bubbly.
10 - Remove foil and bake for an additional 10 minutes until cheese is melted and golden brown. Remove from oven and let stand for 5 minutes before serving. Garnish with extra fresh parsley if desired.