In a large bowl, combine chicken, ¼ cup canned adobo sauce, kosher salt, and black pepper. Refrigerate, uncovered, for at least 30 minutes and up to 24 hours.

In a 12-inch-deep sauté pan or cast-iron skillet, heat oil over medium-high heat until shimmering. Add chicken and cook, stirring occasionally, until lightly browned and cooked through, about 8 minutes. Transfer chicken and any juices to a large plate or bowl and set aside. Do not wipe skillet clean.

Add bacon to now-empty skillet and cook over medium heat, stirring occasionally, until crisped, 8 to 10 minutes. Use a slotted spoon to transfer the bacon to a plate or bowl. You should have about 2 tablespoons (30 ml) of rendered fat in the skillet.

Adjust oven rack to upper-middle position and heat broiler on high. Add onions and mushrooms to rendered fat in skillet and cook over medium heat, stirring occasionally, until onions and mushrooms are beginning to brown, 8 to 10 minutes. Add garlic, cumin, and oregano and cook until fragrant, about 30 seconds. Add chicken stock and scrape bottom of skillet with a wooden spoon to scrape up any browned bits, about 1 minute.

Return cooked bacon, chicken, and any accumulated juices, and remaining minced chipotles to skillet. Cook, while stirring constantly, until all ingredients are warmed through, about 1 minute. Season to taste with salt, if needed. Top with shredded cheese. Broil just until cheese is melted, 2 to 5 minutes. Top with cilantro and serve with warm tortillas.