Make the red chile sauce: Heat chiles in a 12″ skillet over high heat, and cook, turning as needed, until toasted, about 5 minutes; transfer chiles to a blender with chocolate, oregano, cinnamon, crackers, garlic, clove, and 1 1⁄2 cups boiling water, and let sit for 5 minutes. Puree until smooth, and then pour sauce through a fine strainer into a bowl.
Heat 1 tbsp. oil in a 2-qt. saucepan over medium-high heat, and add chile sauce; cook, stirring often, until reduced and thickened, about 6 minutes. Season with salt and set aside.
To assemble the enchiladas, combine the queso añejo and onion in a small bowl and set aside. Pour oil to a depth of 2″ in a 6-qt. Dutch oven and heat over medium-high heat until a deep-fry thermometer reads 350°.
Using tongs, grasp all the tortillas in a stack and submerge in oil, swirling in oil until slightly fried and pliable, about 15 seconds. (The surface of the tortillas should puff up in tiny pockets in several places.) Remove from oil and set aside on a plate to cool. (Alternatively, you may wrap the tortillas in a damp towel towel and briefly microwave to steam.)
Dip each tortilla in chile sauce until completely coated. Transfer to a plate and top with 3 tbsp. cheese filling; roll up like a cigar and sprinkle with more cheese. Serve immediately with rice and beans.