Preheat oven to 350 degrees. Heat a large pot of water to boiling and add in the jumbo shells. Cook until softened but not quite done all the way through, about 12 minutes. Drain, rinse, and set aside to cool. Meanwhile in a medium sized skillet, heat the oil over medium heat. Saute onion and mushrooms for 5-7 minutes or until vegetables are soft and tender. Stir in the spinach, garlic and thyme and cook for another 2-3 minutes. Remove from the skillet and into a large bowl. Add in the ricotta, Parmesan and salt and pepper. Taste for seasoning. Add in the egg. Spoon the cheese filling into a plastic zip-top bag and the cut out one bottom corner to make a piping bag. Pour one jar of the marinara sauce in the bottom of a 9x13 pan. Pipe a couple of tablespoons of filling into each shell and then place them in the pan. Continue until they are all done. Pour the remaining jar of marinara over the shells and sprinkle with Parmesan. Cover tightly with foil and bake until dish is bubbly and pasta is cooked through, 30 to 40 minutes. Serve and enjoy!