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 until al dente according to package directions. 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 fully incorporated.
04 - Melt butter in a saucepan over medium heat. Whisk in flour and cook for 1 minute to form a roux. Gradually whisk in milk and heavy cream until smooth, eliminating any lumps.
05 - Bring mixture to a gentle simmer, stirring frequently, until sauce thickens sufficiently to coat 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 across the bottom of the prepared baking dish.
07 - Fill each pasta shell with approximately 2 tablespoons of the seafood mixture. Arrange stuffed shells in the dish, opening facing up.
08 - Pour remaining sauce evenly over the stuffed shells. Sprinkle mozzarella and Parmesan cheese across the top.
09 - Cover baking dish with aluminum foil and bake for 25 minutes.
10 - Remove foil and continue baking for an additional 10 minutes, or until cheese is bubbly and golden brown.
11 - Allow dish to rest for 5 minutes before serving. Garnish with additional fresh parsley if desired.