Preheat oven to 400 degrees Fahrenheit and butter a 3-quart shallow baking dish. Fill a large pot three-fourths full with water and add a pinch of salt. Cook macaroni until al dente
Melt butter in a sauté pan and add panko breadcrumbs. Season with salt and pepper. Keep stirring over medium heat until golden brown. Let cool and add 1/2 cup of Cheddar until combined.*
In a large saucepan, melt butter over low to medium heat and stir in flour, stirring for 3 minutes. Whisk in milk. Bring sauce to a boil, whisking constantly, and simmer. Whisk occasionally for 3 minutes. Stir in remaining Cheddar, mustard, thyme, salt and pepper. Remove pan from heat.
In a large bowl, stir together macaroni, chicken stock and sauce. Transfer mixture to baking dish.
Sprinkle breadcrumbs and cheese mixture evenly over macaroni and bake in middle of oven for 20 to 25 minutes, or until golden and bubbling.