Preheat the oven to 350 degrees. Spray a 9x13 baking dish with non-stick spray.
Bring 8 cups of water with 1 tablespoon salt to a boil.
While the water is coming to a boil, prepare the sauce by combining the mushrooms and marinara sauce in a medium bowl.
Add the pasta to the boiling water, and cook until al dente, usually about 8 minutes. Drain completely.
While the pasta is cooking, prepare the filling by combining the eggs, ricotta cheese, 1 cup of mozzarella cheese, ½ cup of Parmesan cheese, crushed red pepper, garlic, salt, pepper and 1 tablespoon of the parsley in a large bowl and set aside.
Spread half of the mushroom-marinara sauce into the prepared baking dish.
Fill each shell with 1 tablespoon of the cheese filling and place open side down into the sauce. Repeat with remaining shells until dish is full.
Spread the remaining sauce on top of the shells and then top with the remaining Parmesan and mozzarella cheese. Sprinkle the parsley on top.
Bake for 30 minutes. Optionally, turn on the broiler for a minute or two, to get the cheese browned and crispy.
Remove from the oven and let cool for 10 minutes before cutting into squares and serving. Sprinkle with additional parsley if desired.