Heat the oil in a large Dutch oven over medium-high heat. Add the onion and cook until soft. Add the garlic and red pepper flakes and cook for 1 minute. Add the red peppers and cook for 1 minute.
Add the tomatoes, bring to a boil and cook, stirring occasionally, until thickened, about 25 to 30 minutes. Transfer the mixture to a food processor and process until smooth. Return the mixture back to the pot, add the parsley, basil and oregano and season with salt and pepper. Cook for 10 minutes longer and season with honey, if needed.
To dry out the bread crumbs:
Preheat the oven to 300 degree F.
Evenly spread the bread crumbs on a large baking sheet and place in the oven. Bake for 5 minutes, turn the oven off and let the bread crumbs sit in the oven for 30 minutes or until just dry.
Raise the temperature of the oven up to 400 degrees F. Lightly butter the bottom and sides of a 15 by 10 by 2-inch baking dish and set aside.
Place the bread crumbs into a large shallow bowl. Add the herbs, 1 1/2 teaspoons salt and 1/2 teaspoon of pepper. In another medium shallow bowl, whisk the eggs and 2 tablespoons of water together.
Season each eggplant slice on both sides with salt and pepper. Dredge each eggplant slice in the flour, tapping off excess, then dip it in the egg, and finally dredge it in the bread crumb mixture. Shake off any excess breading and transfer the egg plant to a baking sheet. Repeat with the remaining eggplant.
Heat 1/2-inch of oil in 2 large straight-sided saute pans over medium heat until the oil reaches a temperature of 385 degrees F. Working in small batches, fry a few of the eggplant slices, turning once, until golden brown, about 3 minutes per batch. Using tongs, transfer to a paper towel-lined baking sheet. Repeat with the remaining eggplant.
Cover the bottom of the prepared baking dish with some of the tomato sauce and arrange 1/2 of the eggplant over the sauce. Cover the eggplant with some of the sauce, grated mozzarella, fontina, Romano cheese and some of the basil. Repeat to make 3 layers ending with the sauce. Top with the fresh mozzarella and remaining Romano and bake until hot and just beginning to brown, about 30 minutes. Let rest 10 minutes before serving.