Heat the olive oil in a medium to large sized saucepan or Dutch oven over medium high heat. Add the garlic, oregano and thyme sprigs and allow everything to cook in the olive oil for about 2-3 minutes.

Pour in the crushed tomato sauce and diced tomatoes and mix well. Bring to a boil, turn the heat down to medium-low and let simmer for about 20 minutes. Stirring occasionally.

Season with the red chili pepper flakes and salt and pepper. Mix well and let cook for an additional 10 minutes more. Remove from heat and set aside. Remove the oregano and thyme sprigs and discard.

Cook the jumbo sized pasta shells according to package instructions; cook to al dente only. Remove from heat, drain, rinse and set aside.

Preheat oven to 375 degrees. Using a medium to large sized nonstick skillet over medium high heat, heat the olive oil for about a minute. Add the garlic and onions and sauté for 2-3 minutes. Add the zucchini and mushrooms and cook about 4-5 minutes, until soft and tender. Season with salt and pepper and mix well. Remove from heat and set side.

Using a large mixing bowl, combine the slightly cooled zucchini and mushroom mixture (discarding any liquid) with the ricotta cheese. Mix well. Using a 9x13 casserole baking dish, pour in about 1 cup of the marinara sauce on the bottom, covering the dish.

Stuff the pasta shells with the zucchini, mushroom and ricotta mixture and place open side up or down (your preference) into the baking dish on top of the marinara sauce. Continue until the baking dish is full.

Ladle another 1 to 2 cups of the marinara sauce over the pasta shells and sprinkle the shredded mozzarella cheese over the top. Cover the baking dish with foil and bake for about 25 minutes, or until the inside is heated through. Remove the foil and bake for another 5 minutes or until the cheese is melted nicely. Serve immediately.