In a pot of boiling salted water, cook the pasta until al dente; drain.
Set an extra-large skillet, or a large heavy saucepan, over medium-low heat and cook the bacon until crispy and the fat renders out, 10 to 12 minutes. Set the bacon aside, reserving the fat to build your sauce. At this point you should have about 1/4 cup of reserved fat. If needed, add some olive oil or butter to make sure you have a 1/4 cup of fat in the pan.
Add the flour and cook, whisking constantly, until the paste bubbles a bit, about 2 minutes (make sure it doesn't brown). Continuing to whisk, add 3 cups of the hot milk and cook until the sauce thickens, about 5 minutes. Season with salt and pepper. Bring the sauce to a boil, reduce the heat to low and cook for 2 to 3 more minutes. Stir in the dry mustard, and then gradually add the Cheddar and Muenster cheeses, stirring constantly until all of the cheese has melted into the sauce. Stir in the hot sauce and the remaining 1 cup milk. Add the cooked pasta to the sauce and stir to coat. Stir in the crispy bacon and season with salt and pepper.