Preheat oven to 375°F.
Bring a large pot of cold water to a boil. Season liberally with salt and add in the pasta. Cook until al dente, according to the package directions. Drain and set aside.
Set a large oven-safe skillet over medium high heat with 3 tablespoons butter. Once melted, whisk in the flour and cook for about 30 seconds or so. Slowly stream in the milk, while whisking constantly. Stir in the bay leaves and thyme and cook, stirring occasionally, until thickened, about 5 minutes. Season liberally with salt and black pepper and add the mustard. Remove from the heat and stir in the parmesan and 1 cup of gruyere until melted through. Add the cooked pasta and the ham and stir until well combined.
Make small wells throughout the mac and cheese and carefully crack an egg into each. Top with the remaining gruyere cheese and bake until golden brown and the eggs have set, about 25 to 30 minutes.
Meanwhile, set a small skillet over moderate heat with the remaining butter. Once melted and hot, add the bread pieces and season lightly with salt and pepper. Cook, stirring often, until golden brown and toasted, about 5 minutes. Top the mac and cheese with the toasted bread and garnish with fresh thyme leaves. Enjoy!