PASTA: Cook Shells, Set aside, taking care to keep separate so they won't stick. FILLING: While the Pasta cooks, saute garlic. Add mushrooms, red pepper, thyme, salt and pepper. Cook until mushroom liquid evaporates. Transfer mixture to a large bowl. Add the Tofu and Cheese to the mushroom mixture, and toss to combine thoroughly. Press some of the filling into each of the cooked shells. Set the stuffed shells in a shallow baking dish that has been sprayed with oil. PreHeat the oven to 350 degreesF. SAUCE: Saute scallions for three minutes. Add the fennel, fennel seed, pepper, and salt, and cook the mixture, stirring often, another three minutes. Stir in the tomatoes with their juice and the tomato paste, and cook the sauce 5 minutes longer. Pour the sauce over the stuffed shells, cover the shells with foil, sealing the edges. Put the shells in the hot oven and bake for 15 minutes. Remove the foil, and continue baking the shells for another 5 to 10 minutes, or until dish is heated through.