Bring a large pot of salted water to a boil. Add the pasta and cook to al dente according to the package instructions. Drain the pasta and rinse under cold water; set aside.
Meanwhile, combine the ricotta, Parmesan, parsley, egg, 1/2 cup of the mozzarella, a large pinch of salt and a few grinds of pepper in a large bowl. Fold to combine; set aside.
Preheat the oven to 450 degrees F.
Heat a 12-inch ovenproof skillet over medium-high heat. Add the bacon and cook, stirring occasionally, until crisp and brown, about 3 minutes. Remove with a slotted spoon to a paper towel-lined plate and reserve.
Add the sausage to the skillet and cook, breaking it up with a wooden spoon into large chunks, until brown, about 5 minutes. Remove half the sausage from the skillet with a slotted spoon to a plate and reserve.
Add the ground beef and onion to the skillet and cook until the beef is brown and the onion is translucent, about 5 minutes. Add the garlic and cook until fragrant, about 1 minute more. Add the marinara sauce and season with 1/2 teaspoon salt and a few grinds of pepper. Bring to a simmer, reduce the heat to low and continue to simmer while you stuff the shells.
Divide the ricotta filling among the shells. Arrange the shells filling-side up in the skillet on top of the sauce. Top with the remaining mozzarella, the pepperoni and reserved sausage and bacon. Bake until the cheese is melted and the toppings are browned, 20 to 25 minutes. Sprinkle with Parmesan, oregano and red pepper flakes before serving.
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