In a large mixing bowl, combine the lime juice, salt, cumin, chipotle pepper, cilantro and garlic to make the marinade.
Add the chicken breast cubes to the marinade, toss to coat the chicken in the marinade.
Place in the refrigerator for 30 minutes to marinate.
After the chicken has marinated, skewer the chicken, bell peppers and onions onto 12 metal or wooden skewers. If using wooden skewers, be sure to soak them for at least 30 minutes ahead of time.
Place the skewers on the grill over medium heat for 5-7 minutes, flip and grill for an additional 5-7 minutes.
After the chicken is cooked through, remove from the grill, squeeze the additional lime over the skewers and serve.
Marinating the chicken: the chicken should not be marinated for more than two hours. The acid from the lime juice will break down the texture of the chicken if it's marinated for more than 2 hours, making it mushy instead of tender. Also, never marinate chicken with citrus in a metal bowl. The acid from the citrus can react to the metal and ruin the chicken.
Make these fajitas in the oven: Toss the onions and bell pepper in with the chicken in the marinade. After 30 minutes, remove the veggies and chicken. Discard the marinade. Arrange the chicken and veggies in an even layer on a foil-lined baking sheet. Place in a 400°F oven for 15-20 minutes.
Make these fajitas on the stove: Prepare the marinade and marinate the chicken as instructed. After the chicken has marinated, add 1 tablespoon olive oil to a large skillet over medium high heat. Add the bell peppers and onions, sauté for 3-5 minutes. Drain the chicken and discard the marinade, then add the chicken to the skillet and sauté for 6-8 minutes.