Preheat the oven to 400 degrees Fahrenheit (204 C).
Place the cubed squash on a baking pan evenly. Drizzle the squash with oil and sprinkle with salt and pepper. Bake for 25-30 or until the squash is fork tender.
Transfer the squash to a high powered blender and add the milk, thyme, oregano, and crushed red pepper. Blend until the sauce is smooth and creamy. Taste sauce and add additional seasoning if needed.
Bring a large pot of salted water to boil. Cook according to the back of the package. Drain water, and set aside.
In a large bowl crumble the tofu with a spoon or your hands breaking into small pieces. Add the milk, lemon juice, nutritional yeast, spinach, dried thyme, dried oregano, garlic powder, salt, pepper, and mix.
Coat the 9 x 13 inch baking dish with the butternut squash sauce.
Assemble pasta shells by filling each shell with the tofu ricotta mixture, around 1-2 tablespoons. Place the stuffed shells facing up in the baking dish.
Sprinkle shells with vegan mozzarella cheese and bake for 10-15 minutes or until hot and bubbly. Top with crushed red pepper and fried sage.