Make the sauce: Heat the olive oil in a large skillet over medium-high heat. Add the garlic, fennel seeds and red pepper flakes and cook, stirring, until the garlic is lightly golden, about 1 minute. Add the tomatoes and 1 teaspoon salt; cook, stirring occasionally, until the tomatoes begin to sizzle, about 5 minutes. Add half of the basil and 1/2 cup water and bring to a boil. Reduce the heat to medium low and simmer, stirring occasionally and smashing the tomatoes with the back of a spoon, 25 minutes. Stir in the remaining basil and season with salt.
Prepare the zucchini: Preheat the oven to 400 degrees F. Trim the zucchini and halve crosswise, then slice lengthwise into 18 strips, about 1/4 inch thick. Put the flour in a shallow dish. Whisk the eggs and milk in another dish. In a third dish, combine the panko, parmesan, parsley, garlic, 1/2 teaspoon salt, and pepper to taste. Working in batches, dredge the zucchini in the flour and shake off the excess. Dip in the egg mixture, turning to coat; let the excess drip off, then dredge in the panko mixture, pressing to help it stick. Set aside.
Heat the olive oil in a large, deep skillet over medium-high heat. Working in batches, add the zucchini in a single layer and fry until golden brown, 2 to 3 minutes per side. Drain on paper towels; season with salt.
Lay 6 pieces fried zucchini a few inches apart in a 9-by-13-inch baking dish. Top each with a few tablespoons of the tomato sauce, a slice of mozzarella and a piece of prosciutto. Repeat the layering (zucchini, sauce, mozzarella, prosciutto), then top with the remaining zucchini. Top with a little more sauce, sprinkle with parmesan and dollop with the ricotta. Bake until heated through, about 15 minutes. Top the stacks with more prosciutto. Serve with the remaining sauce.