Make the sauce:
Stack five slices of the pepperoni, cut into thin strips, then cut crosswise into tiny pieces. Heat the oil over medium heat in a large, heavy saucepan. Add the onions and cook, stirring, until lightly golden, 8 to 9 minutes. Add the garlic, chopped pepperoni, oregano, thyme, and chili flakes and cook, stirring, until the pepperoni renders some of its fat and the garlic is fragrant, 2-3 minutes. Add the tomato paste and cook, stirring, until caramelized, 2-3 minutes. Add the crushed and diced tomatoes and 1 tablespoon of the salt, bring to a boil, reduce the heat to low, add the basil and simmer, stirring occasionally, until the sauce thickens and reduces by about 25 percent, 35-40 minutes (you should have about 7 cups sauce). Season with more salt to taste.
While the sauce is simmering, combine the ricotta, eggs, parm, parsley, remaining 1 ½ teaspoons salt, pepper, and lemon zest in a large bowl and mix to combine. Bring a large pot of generously salted water to a boil in a large pot. Using the package directions as your guide, cook the noodles two minutes less than al dente; drain and coat lightly with oil to prevent sticking.
Arrange a rack in the top third of the oven and preheat the oven to 350°F. Ladle one cup of the sauce on the bottom of the Cravings 13 x 10 baking pan (or other 9 x 13 inch baking dish). Arrange three noodles lengthwise in the bottom of the pan, ladle another cup of sauce on top of the noodles. Dollop one third of the ricotta mixture on top all over the sauce, then sprinkle with one cup of the shredded mozzarella cheese. Repeat with another layer of sauce, ricotta mixture, and shredded mozzarella three more times. Top with a final layer of noodles, then with a generous cup of sauce, and evenly distribute the fresh mozzarella rounds on top of the sauce, followed by the remaining two ounces of pepperoni.
Cover tightly with foil and bake for 40 minutes. Uncover and bake until the cheese and sauce are bubbly and the pepperoni begins to curl slightly, another 25 to 30 minutes. Raise the oven heat to broil and broil until the top is deep golden, making sure not to burn the top, 3-4 minutes. Remove from the oven, let cool for 15 minutes, then cut into 12 pieces and serve.