Preheat the oven to 375°F.
Cook the jumbo pasta shells according to package instructions until al dente. Drain and set aside.
In a large skillet, heat olive oil over medium heat. Add the chopped onion and sauté until translucent, about 3-4 minutes.
Stir in the minced garlic and cook for an additional minute.
Add the sliced mushrooms, thyme, oregano, salt, and pepper to the skillet. Cook until the mushrooms are tender and have released their moisture, about 5-7 minutes. Remove from heat and let cool slightly.
In a large bowl, combine the ricotta cheese, half of the mozzarella cheese, Parmesan cheese, and chopped parsley. Stir in the mushroom mixture until well combined.
Spread 1/2 cup of marinara sauce on the bottom of a 9x13-inch baking dish.
Stuff each cooked pasta shell with the mushroom and cheese mixture and place them in the baking dish.
Pour the remaining marinara sauce over the stuffed shells and sprinkle with the remaining mozzarella cheese.
Cover the baking dish with aluminum foil and bake for 25 minutes.
Remove the foil and bake for an additional 10-15 minutes, or until the cheese is bubbly and golden.
Let cool for 5 minutes before serving.