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 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 uniformly combined. Refrigerate until ready to use.
04 - Melt butter in a saucepan over medium heat. Whisk in flour and cook for 1 minute to form a roux, stirring constantly to prevent browning.
05 - Slowly whisk in whole milk and heavy cream until smooth. Bring to a gentle simmer, stirring frequently, until sauce thickens and coats the back of a spoon, approximately 3-4 minutes.
06 - Remove from heat. Stir in Parmesan cheese, lemon zest, lemon juice, nutmeg, salt, and pepper until cheese melts completely.
07 - Spread one-third of the white sauce evenly across the bottom of the prepared baking dish.
08 - Stuff each pasta shell with approximately 2 tablespoons of the seafood mixture. Arrange filled shells open side up in rows within the baking dish.
09 - Pour the remaining white sauce evenly over the stuffed shells, ensuring each shell is coated. Sprinkle mozzarella and additional Parmesan cheese across the top.
10 - Cover baking dish tightly with aluminum foil. Bake for 25 minutes until heated through and sauce bubbles around edges.
11 - Remove foil and continue baking for an additional 10 minutes until cheese is golden brown and bubbly.
12 - Let stuffed shells rest for 5 minutes before serving to allow filling to set. Garnish with additional fresh parsley if desired.