Bring a large pot of salted water to a boil and add the jumbo shells. You may need to do this in batches depending on how large your pot is. Cook until just al dente according to package directions, set aside. Drain, reserving 1 cup pasta water.
While the water is boiling, heat oil in a large skillet over medium heat. Add the sage and stir to crisp, about 30 second 1 minute. Remove sage with a slotted spoon and place in a bowl. Sprinkle lightly with sea salt and set the bowl aside.
Add the squash, onion, garlic and red pepper flakes to the same skillet along with a pinch of salt and pepper. Cook, stirring often, until onion is tender, about 10 minutes.
Add in the vegetable broth and bring mixture to a boil. Reduce heat to low and simmer until squash is fork tender and liquid is reduced by half, about 20 minutes. Remove from heat and cool slightly. Using an immersion blender, blender, or food processor, puree the sauce until velvety smooth along with 1/3 cup reserved pasta water. If it’s too thick, add in more pasta water. It should be the consistency of jarred marinara.
Meanwhile, make the tofu ricotta. Heat a large skillet over medium heat and crumble the tofu in. Cook for 2-3 minutes to remove any excess water. Add in the olive oil, lemon juice, parsley, nutritional yeast, oregano, garlic powder and salt. Stir to combine, set aside.
Preheat the oven to 375 degrees F.
To assemble the stuffed shells, place 1 cup of the butternut sauce on the bottom of a 9×13″ pan. Spoon a large dollop of the tofu mixture into each shell and place in the dish. Continue with the rest of the shells, then top with the remaining butternut sauce.
Cover will foil and bake for 25 minutes.
Remove. Garnish with toasted pecans and reserved crispy fried sage.