Preheat oven to 400 degrees. Chop bacon and cook until crisp. Remove the bacon from the pan and add the onion, chopped mushroom stems, fresh thyme, parsley, and salt and pepper to taste. Sauté for 4-5 minutes on medium-high heat then add the bread, and toss over heat for an additional 1-2 minutes until well combined. Remove from the heat and add the shredded Gouda (reserving some for the top), Parmesan, half and half, beaten eggs, and the reserved chopped bacon. Layer a thin layer of the Gouda in the bottom of each mushroom and generously salt and pepper. Fill with the Bacon Gouda Stuffing and top with additional Gouda and cracked black pepper. Bake for 20-22 minutes until the cheese is golden brown. Garnish with freshly chopped parsley and serve immediately. Enjoy!