Preheat the oven to 375 degrees F.
In medium-high heat, heat a large sauté pan. Add the oil and the onions, garlic, mushrooms, basil, oregano, red pepper flakes, and 1/2 teaspoon of salt when heated. Sauté for 5 mins or until the mushrooms are softened, stirring occasionally. Before continuing to step 3, make sure all the liquid has evaporated from the mushrooms.
Stir in the spinach and cook until the spinach is wilt. Remove the pan from the heat and mix in the cooked chicken. Put it aside.
In a small saucepan, mix chicken broth, milk, nutmeg, and 1 teaspoon of salt remaining. Bring to a slow simmer over medium heat. As soon as the mixture begins to bubble up around the edges, gradually whisk in the flour and simmer until thickened, around 10 minutes. Stir in Parmesan cheese and remove from heat.
In the bottom of the 10X10 square baking dish, place 1/2 cup sauce, top with 2 noodles, 1 cup chicken mixture, 1 cup mozzarella sauce, and 1/4 cup mozzarella, making sure the noodles are sauce-coated. Also, you can gently press it down. Repeat with three more layers of noodles, chicken, cheese, and sauce. Then there will be a little more sauce in the last layer and the remaining cheese on top.
Cover the baking dish with aluminum foil and bake for about 25 minutes. Uncover and bake for a further 15 min. If necessary, broil the golden brown top for 2-3 minutes. Let stand about 5 minutes before serving.