Place 3/4 of the Tofu in a Food Processor or Blender and add 2 tablespoons of Olive Oil, a pinch of Nutmeg, nutritional yeast, and 1/4 teaspoon of sea salt. Blend until smooth. Mash the remaining Tofu into the Blended mixture that resembles Ricotta cheese or cottage cheese. Set aside.
Preheat Oven to 350 degrees.
Sauté the onion in a little Olive Oil till it becomes translucent, but not browned then add the garlic and sauté for just a minute more. If using frozen spinach just defrost the spinach do not cook. If using fresh spinach steam until the spinach is wilted about 2 minutes in boiling water. Make sure in both instances to squeeze out all of the excess liquid. Add the spinach, onion and seasonings to the Ricotta mixture and set aside. Can be made ahead and refrigerated up to 24 hours.
In a large pot boil the Shells as directed on the package. Drain and rinse under cold water to cool off enough to handle them. Place enough spaghetti sauce on the bottom of an 8 X 12 baking dish just to cover. Stuff the shells with the Ricotta mixture. When you are done stuffing the shells place the rest of the spaghetti sauce over the shells. Cover with foil and bake for 30 minutes. Let cool for at least 10 minutes before serving.