In a large sauce pan, add about 2 teaspoons of salt to 4 quarts of water over high heat to bring to a boil. Add macaroni to boiling water for 7 minutes, stirring occasionally. Drain in colander and toss with small amount of olive oil to prevent sticking.
In a prep bowl, combine flour, salt, pepper, and ground mustard.In the same sauce pan used for the macaroni, make a roux by melting butter and slowly sprinkling in the flour mixture while whisking. Cook over medium-low heat for 2 to 3 minutes while while whisking until the roux turns golden brown.
Whisk milk into roux a little at a time, whisking constantly to blend evenly and prevent lumps. Add cheeses and cook over medium heat while stirring until cheese has melted. Stir in macaroni until evenly coated with cheese sauce.The cheese sauce will be thin at this point. Let the macaroni sit for 10-15 minutes to thicken.
Place baking cups in a muffin pan. Stir macaroni to evenly distribute sauce and divide equally into baking cups. (A measuring cup works well.)
Sprinkle 1 tablespoon of cheddar jack cheese on ⅓ of the cups. Top ⅓ of the cups with the bacon pieces; top ⅓ of the cups with the panko bread crumb mixture.
Bake at 375 degrees F for 10-15 minutes or until cheese is melted and toppings are beginning to brown. Top with fresh chopped parsley before serving.