Bring 6 quart of water to a boil. Add salt and add in the pasta and cook to al dente. Do not overcook the pasta as we will be baking this in the oven later. Drain the water off and set aside. Do not rinse the pasta.
Preheat a large skillet with some oil. Add in onion and saute for about 5 minutes until soft and fragrant. Add in thered pepper flakes and garlic and saute for about 1 minute. Add in Italian sausage and use spatula to break up the meat into smaller pieces. Cook until the meat turn brown. Add in the prosciutto and pepperoni and stir to mix everything. Remove from the heat
Preheat oven to 425 F. Get a 9 x 13 inch casserole dish/pan. Spread about 1 cup of marinara sauce on the bottom of the dish. Spread about 1/3 of the sausage mixture on top followed by 1/3 of ricotta cheese. You can dot them all over the place of spread them evenly. It's up to you. Then top with 1/3 of the cooked penne and sprinkle with some Parmesan and Mozzarella cheese. Repeat the second layer with the same sequence. You can probably get to 3 or 4 layers. You will finish up with Parmesan and Mozzarella cheese covering up the very top. Pop this into oven (3rd rack from the top) and bake for about 15-20 minutes or until the cheese is bubbly and golden brown
Let the Penne Al Forno rest for about 1 minute before serving immediately.