Preheat the oven to 350°.
Heat a large oven-safe skillet over medium-high heat then add in the oil. Season the chicken all over with salt and pepper, add it to the skillet, and cook turning once, until browned, about 12 minutes. Transfer the chicken to a paper towel-lined tray. Turn the skillet down to medium-low heat.
Add the onion and garlic to the skillet, cook, stirring occasionally, until the onion is lightly browned and softened, about 5 minutes. Add the cumin and chipotle peppers and cook until fragrant, 2 minutes. Next, add the can of crushed tomatoes and beer then bring to a simmer. Return the chicken to the skillet then place the whole pan in the oven, uncovered for 45 minutes, turning the chicken half-way through.
Remove the chicken from the sauce and once it's cool enough to handle shred the meat and discard the bones. Transfer the sauce to a food processor or blender and let cool for 15 minutes. Puree until smooth and season with lime juice, salt, and pepper. Return the shredded chicken to the skillet and pour the sauce over the chicken.
Warm the tortillas by placing them directly over a gas flame to char the edges. Place on a plate, and cover with a towel to steam.
To assemble, spoon about 3 tablespoons of chicken onto each tortilla top with crumbled cheese and chopped cilantro, serve immediately!