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In a large pot of boiling water, cook the jumbo pasta shells according to the prebake cooking directions on the package. Then drain, rinse with cold water to prevent sticking, and set aside.
Meanwhile, in the bowl of a food processor, combine the tofu, onion, garlic, basil, oregano, salt, black pepper, red chili pepper flakes (if using), nutritional yeast, and lemon juice. Pulse 15 times or until partially mixed. Add the spinach and pulse just a few more times until combined. The resulting texture should be ricotta-like. Do not over pulse or your ricotta will turn green!
Preheat the oven to 375 degrees F. Pour half of the marinara sauce into a 9 × 13-inch baking dish, spreading to evenly coat the bottom of the dish.
One by one, fill each cooked shell with a generous spoonful of the tofu ricotta filling and place in the prepared baking dish. Continue until the tofu mixture is gone and the baking dish is filled. Sprinkle the vegan cheese (if using) on top.
Drizzle the remaining marinara sauce over the stuffed shells. Cover the pan with aluminum foil and bake for 20 minutes. Remove the foil and bake for another 20 minutes or until the cheese (if using) is melted and the edges of the shells are lightly browned. Garnish with the basil leaves (if using). Serve immediately and enjoy hot.