To make the sauce: Heat oven to 350'F. In a pot, heat oil and saute garlic, onions and hot-pepper flakes until golden. Stir in tomato paste. Rinse can with the water and add to pot. Simmer 30 minutes. Add all the remaining ingredients. Simmer at least 1-1/2 to 2 hours. If you have more time, let it simmer even a little longer.
To make the filling: Combine ricotta, pepper, parsley and eggs in medium bowl. Mix thoroughly. Reserve cheeses. To assemble the casserole: Cook rigatoni according to package directions, but reduce cooking time by two minutes. Do not overcook. Spread sauce over the bottom of a 9x13x2" baking dish. Top with a layer of pasta. Top pasta with a little more sauce, then several spoons full of ricotta mixture. Spoon together with the back of a large spoon. Top with a sprinkling of mozzarella cheese. Top with a layer of pasta and repeat process, ending with Parmesan this time. Then repeat, ending with mozzarella, etc. Finish with a layer of pasta. Bake for 30-35 minutes, or for about 15 minutes after it begins to bubble around edges. Ricotta will rise to top; it should be slightly set. Allow to stand 10-15 minutes before serving. Serves six to eight.