Cook the pasta: Bring a large pot of salted water to a boil. Add the jumbo pasta shells and cook 1 minute less than the package instructions for al dente texture. Drain the shells using a colander and set them aside to cool.
Sauté the aromatics: Heat 1 teaspoon of olive oil in a large skillet over medium heat. Add the chopped onions and garlic and cook for 2 to 3 minutes, until softened and fragrant.
Cook the meat: Add the ground pork to the skillet. Season with salt, pepper, Italian seasoning, and red pepper flakes. Cook for 5 to 7 minutes, breaking it up with a spoon until browned and cooked through.
Make the filling: In a large mixing bowl, combine the cooked ground pork, ricotta cheese, 8 ounces of shredded mozzarella, egg, thawed and well-squeezed spinach, and ¼ cup of parmesan cheese. Mix well until evenly blended.
Stuff the shells: Fill each cooked and cooled pasta shell with about 2 heaping tablespoons of the meat mixture, making sure they are generously filled.
Prepare the sauce: Pour half of the marinara sauce into the bottom of a large baking dish (or 2 smaller dishes).
Assemble the dish: Arrange the stuffed shells in the baking dish over the sauce. Pour the remaining marinara sauce over the top of the shells. Sprinkle additional shredded mozzarella and parmesan cheese evenly over the top.
Bake the dish: Preheat the oven to 375 degrees Fahrenheit. Cover the dish with foil and bake for 30 minutes. Remove the foil and bake for an additional 10 to 15 minutes, or until the cheese is golden, bubbly, and slightly crispy on top.
Serve and garnish: Let the dish cool for a few minutes before serving. Spoon extra sauce from the baking dish over the stuffed shells before plating. Garnish with fresh basil if desired.