For the Carnitas: Heat oven to 225°F. In a large hotel pan, add pork shoulder. Cover halfway up with pork fat. Add remaining ingredients. Mix pork is evenly coated. Cover pan with aluminum foil and roast 8 hours, or until fork-tender.
For the Salsa Roja: In a rondeau over medium flame, heat a splash of oil. Add chiles and a pinch of black peppercorns. Toast until fragrant. Add garlic and onions. Cook until alliums are soft and translucent. Add tomatoes and sugar. Reduce heat and let simmer 2 hours, stirring occasionally. Transfer mixture to a Vitamix Commercial blender and purée until smooth. Let cool. Transfer to an airtight container and refrigerate.
To Assemble and Serve: On a work surface, stuff each pepper with ½ cup Chihuahua cheese and 4 ounces Carnitas. Close peppers and transfer to a sheet tray. Top with Cotija cheese. Drizzle with agave syrup and chile oil. Finish with pepitas. Using a blowtorch, char the tops until the cheese has melted and is bubbly. Transfer to a serving plate. Top with sour cream and serve with a ramekin Salsa Roja.
