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1. Spray a baking sheet lightly with cooking spray. Bring a large pot of salted water to a boil. Add the shells, and partially cook 6 to 7 minutes - they should have started to become tender but will still be firm to the bite. Drain in a colander, and immediately transfer to the oiled baking sheet, spreading them out in a single layer so that they don't stick together. Let cool.
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2. For the sauce, pour the tomatoes into a bowl and mash with your hands, or pulse in food processor to chop. Heat the oil in a large saucepan over medium-low heat. Add the onion and garlic. Cook, stirring, for 1 minute. Cover, reduce heat to very low and cook until vegetables are softened, about 5 minutes. (Check a few times during cooking; if vegetables begin to brown, add 2 teaspoons water and stir.) Add the tomatoes with juice, basil and 1/2 teaspoon salt. Bring to a simmer, cover and simmer gently 5 minutes. Then simmer very gently, partially covered, until thickened, about 20 minutes. Season with 1/8 teaspoon pepper. Scrape into another container with a rubber spatula; set aside.
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3. Add the spinach and 1/2 teaspoon salt to the skillet. Place over medium heat, cover and cook, tossing every now and then with tongs for even cooking, until wilted, 5 to 6 minutes. Drain, and let cool, then squeeze out as much liquid as you can, and chop. Transfer to a bowl; set aside.
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4. In the same skillet, heat the oil over medium heat. Add the zucchini and 1/4 teaspoon salt and cook, stirring every now and then, until tender and lightly browned, 5 to 7 minutes. Add scallions during the final 1 minute. Add to the bowl with the spinach. Add the ricotta, the ham, 1/2 cup of the mozzarella, the parsley, 1/8 teaspoon pepper and the nutmeg, and stir to combine.
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5. Preheat the oven to 350 degrees. 6. Spoon a thin layer of sauce over the bottom of two 9-x-13-inch baking dishes. Fill the cooked shells with 1 tablespoon per shell, and arrange the shells side by side in a single layer
