Bring a large pot of salted water to a boil. Cook elbow macaroni until al dente. Drain and set aside.
In a shallow dish, combine 1 cup flour, paprika, and salt. Dredge chicken cubes in flour, dip into beaten eggs, and dredge again in flour for a double coating.
Heat 2 inches of oil in a heavy-bottomed skillet to 350°F (175°C). Fry chicken in batches for 5-7 minutes until golden brown and internal temperature reaches 165°F (74°C). Drain on a wire rack.
In a small saucepan over medium heat, whisk honey, soy sauce, apple cider vinegar, and cracked black pepper. Simmer for 5 minutes until the glaze coats the back of a spoon. Toss fried chicken in the glaze.
In a large heavy pot, melt butter over medium heat. Whisk in 1/4 cup flour and cook for 2 minutes without browning.
Slowly temper the roux by whisking in milk 1/2 cup at a time until the sauce is smooth and thickened.
Reduce heat to low. Gradually fold in cheddar and mozzarella cheeses until completely emulsified and smooth.
Fold the cooked macaroni into the cheese sauce until evenly incorporated.
Serve the mac and cheese immediately, topped with a generous portion of the glazed honey pepper chicken.