01 - Preheat oven to 350°F. Lightly grease a 9 x 13-inch baking dish with cooking spray or butter.
02 - Boil jumbo pasta shells in salted water according to package directions until al dente. Drain and rinse under cold water to stop cooking process. 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 thoroughly until all ingredients are well incorporated.
04 - Melt butter in a saucepan over medium heat. Whisk in flour and cook for 1 minute to form a roux. Slowly whisk in milk and heavy cream until smooth, eliminating any lumps.
05 - Bring sauce to a gentle simmer, stirring frequently, until thickened approximately 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.
08 - Pour remaining white sauce evenly over all shells. Sprinkle mozzarella and additional Parmesan cheese across the top.
09 - Cover baking dish with aluminum foil. Bake for 25 minutes.
10 - Remove foil and continue baking for 10 additional minutes, or until sauce is bubbly and cheese topping is golden brown.
11 - Let dish stand for 5 minutes before serving to allow filling to set. Garnish with additional fresh parsley if desired.