Preheat oven to 350 degrees. Bring a large pot of lightly salted water to a boil. Add pasta and cook for 8 to 10 minutes or until al dente. Drain pasta and let cool. Heat skillet over medium heat and add onions, cooking for about 3 minutes. Add garlic for a minute, then add sausage and cook for 5 minutes. Add mushrooms and continue cooking until soft. In a large bowl, mix eggs, ricotta, half of the mozzarella, half of the parmesan, fresh herbs, salt, pepper, and cayenne until well combined. Stuff cooked shells with cheese and herb mixture. Place shells in oiled 9x3 inch baking dish. In a medium bowl, stir together pasta sauce, mushrooms, sausage mixture, and the reserved cheese. Pour over shells. Bake in preheated oven 45 to 60 minutes or until edges are bubbly and shells are slightly set.