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Partially cook the pasta shells in a large pot of boiling salted water until slightly tender but still quite firm to the bite, about 4 to 6 minutes. You will continue cooking the shells in the oven after they have been stuffed. Using a slotted spoon, drain pasta shells and place on oiled baking sheet, spreading them out so that they don't stick together and allow to cool.
Heat the oil in a heavy medium saucepan over medium heat. Add the pancetta and saute until golden brown, about 5 minutes. Add the red pepper flakes. Add the garlic and saute until tender, about 1 minute. Add the marinara sauce. Bring the sauce to a simmer, stirring often.
Preheat the oven to 350 degrees F.
Spoon 1 1/4 cups of the sauce over the prepared baking dish. Fill the cooked shells with the cheese mixture, about 2 tablespoons per shell. Arrange the shells in the prepared dish. Spoon the remaining sauce over the shells, then sprinkle with the mozzarella.
Bake in the lower third of your oven until the filling is heated through and the top is golden brown, about 25 to 30 minutes.