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. 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 until thoroughly blended.
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.
05 - Bring sauce to a gentle simmer, stirring frequently, until thickened (3-4 minutes). Stir in Parmesan, lemon zest, lemon juice, nutmeg, salt, and pepper. Remove from heat.
06 - Spread ⅓ of sauce over bottom of baking dish. Fill each shell with seafood mixture (about 2 tablespoons per shell) and arrange open side up in dish.
07 - Pour remaining sauce evenly over shells. Sprinkle with mozzarella and Parmesan.
08 - Cover with foil and bake for 25 minutes.
09 - Remove foil and bake an additional 10 minutes, or until bubbly and golden brown.
10 - Let stand for 5 minutes before serving. Garnish with extra parsley if desired.