Whisk together the chipotle peppers, adobo sauce, garlic, olive oil, cumin, oregano, chili powder, smoked paprika, onion powder, lime juice, vinegar, salt, and pepper in a bowl. Pour over the chicken thighs and toss to coat, then cover and refrigerate for at least 30 minutes, or up to 4 hours for deeper flavor.
In a medium saucepan, heat 1 teaspoon olive oil over medium heat, add the rinsed rice, and toast for 1 minute. Add water or broth and salt, bring to a boil, then reduce to the lowest heat, cover, and cook for 15 minutes undisturbed, followed by 5 minutes off heat. Fluff with a fork and stir in lime juice and cilantro.
Combine the drained black beans, minced chipotle pepper, cumin, lime juice, and water in a small saucepan over medium-low heat. Stir and heat for 5 to 7 minutes until warmed through and flavorful, then season with salt and keep covered.
Combine the diced tomatoes, red onion, jalapeño, lime juice, and cilantro in a small bowl, season with salt, and let sit for at least 10 minutes at room temperature for the flavors to meld.
Scoop the avocado flesh into a bowl, add lime juice immediately, and mash to a slightly chunky consistency. Fold in the red onion, cilantro, salt, and optional cayenne, then press plastic wrap directly against the surface and refrigerate until needed.
Heat a cast iron grill pan or skillet over medium-high heat until very hot, then add the marinated chicken thighs in a single layer. Cook for 5 to 6 minutes per side without moving until charred and the internal temperature reaches 165°F (74°C), then rest for 5 minutes before dicing into bite-sized pieces.
Heat each flour tortilla in a dry skillet over medium heat for 20 to 30 seconds per side until pliable, or wrap all four in a damp paper towel and microwave for 30 seconds.
Layer rice, black beans, diced chicken, cheese, sour cream, pico de gallo, guacamole, and optional lettuce in the center of each warm tortilla, leaving a 2-inch border. Fold the sides in, then roll from the bottom up, keeping the sides tucked, and wrap tightly in foil seam-side down.