Step 1: Cook the jumbo pasta shells according to package directions until al dente. Drain and rinse immediately with cold water to prevent sticking. Set aside.
Step 2: In a large skillet, cook the diced bacon over medium heat until crispy. Remove the bacon with a slotted spoon and set aside on a paper towel-lined plate, reserving 1-2 tablespoons of bacon fat in the skillet.
Step 3: Add the thinly sliced shallots to the skillet with the reserved bacon fat. Cook over medium-low heat for 8-10 minutes, stirring occasionally, until the shallots are soft, translucent, and lightly caramelized. Remove from heat and let cool slightly.
Step 4: In a large mixing bowl, combine the ricotta cheese, 1 cup of Parmesan cheese, the egg, chopped fresh parsley, and nutmeg. Season with salt and pepper. Fold in the cooked crispy bacon and caramelized shallots until well combined.
Step 5: Preheat your oven to 375°F (190°C). Pour half of the marinara sauce into the bottom of a 9x13 inch baking dish, spreading it evenly.
Step 6: Carefully fill each cooked pasta shell with the ricotta-bacon-shallot mixture. Arrange the filled shells in a single layer in the prepared baking dish.
Step 7: Spoon the remaining marinara sauce evenly over the stuffed shells, ensuring each shell is well-covered. Sprinkle generously with additional Parmesan cheese.
Step 8: Cover the baking dish loosely with aluminum foil and bake for 25 minutes. Remove the foil and continue baking for another 10-15 minutes, or until the sauce is bubbly and the cheese is melted and golden brown.
Step 9: Let the Shallot, Bacon & Parmesan Stuffed Shells rest for 5-10 minutes before serving. Garnish with extra fresh parsley if desired.