01 - Preheat oven to 350°F. Lightly grease a 9 x 13-inch baking dish with butter or cooking spray.
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 - Combine shrimp, crab, ricotta, cream cheese, Parmesan, egg, parsley, chives, garlic, salt, pepper, and red pepper flakes in a large bowl. Mix thoroughly until fully incorporated.
04 - Melt butter in a saucepan over medium heat. Whisk in flour and cook for 1 minute, stirring constantly to prevent burning.
05 - Slowly whisk in milk and heavy cream until smooth. Bring to a gentle simmer, stirring frequently, until sauce thickens approximately 3–4 minutes.
06 - Stir in Parmesan, lemon zest, lemon juice, nutmeg, salt, and pepper. Remove from heat immediately.
07 - Spread one-third of the sauce evenly over the bottom of the prepared baking dish.
08 - Fill each pasta shell with approximately 2 tablespoons of seafood mixture. Arrange stuffed shells open side up in the baking dish.
09 - Pour remaining sauce evenly over shells. Sprinkle mozzarella and additional Parmesan cheese across the top.
10 - Cover dish with aluminum foil and bake for 25 minutes.
11 - Remove foil and bake an additional 10 minutes until cheese is bubbly and golden brown.
12 - Let stand for 5 minutes before serving to allow flavors to set. Garnish with extra parsley if desired.