In a smal bowl combine the ingredients for the marinade: lime juice, vegetable oil, Worcestershire sauce, 1 tablespoon ground cumin, 1 tablespoon chili powder, 1 tablespoon fresh chopped cilantro, minced garlic,1 teaspoon brown sugar, ½ teaspoon smoked paprika, ½ teaspoon kosher salt, ½ teaspoon black pepper, ½ teaspoon cayenne pepper, ¼ teaspoon red pepper flakes.
In a large bowl combine the bell peppers and yellow onion. Pour ¾ of the marinade over the vegetables and toss. Place the chicken breast in the small bowl with the remaining marinade and coat the chicken in the marinade. Cover both bowls with plastic wrap and refrigerate for at least 2 hours.
When the chicken and vegetables are done marinating, grill the chicken until it reaches an internal temperature of 165 degrees. Remove from the grill and allow to rest.
Pre-heat oven to 400 degrees. Begin cooking the pasta according to the package directions. While the pasta is cooking, prepare the cheese sauce.
Melt 4 tablespoons of butter in a large saucepan over medium heat. Stir in the flour until smooth, then gradually add the milk. Increase temperature to medium high and bring to a boil. Cook and stir for 2 minutes.
Reduce the heat to medium. Add the cream cheese, 8 ounces cheddar cheese, 1 tablespoon cumin, 1 tablespoon chili powder, ½ tablespoon paprika, ½ teaspoon kosher salt, ½ teaspoon black pepper, ½ teaspoon cayenne pepper, ¼ teaspoon red pepper flakes. Stir until cheese is melted and the sauce is smooth.
Drain the macaroni noodles. Dice the chicken into 1-inch pieces. Combine the cooked macaroni, cheese sauce, chicken and marinated vegetables and stir until everything is evenly coated.
Transfer to a large baking dish. Sprinkle the remaining shredded cheese on top of the macaroni mixture. In a small bowl melt the remaining butter. Toss with the panko bread crumbs and the cilantro and sprinkle over the cheddar cheese. Bake uncovered 15-20 minutes, or until the top is golden brown.