To prepare the pork shoulder, in a sauté pan, toast the ancho chiles and chipotle chiles until fragrant and browned, about 4 minutes. Add the wine and bring the mixture to a quick boil. Remove from the heat and let cool, then transfer the chile mixture to a blender. 

In the same pan, warm the vegetable oil. Add the cumin seeds and oregano and cook, stirring frequently, until fragrant, 1 to 2 minutes. Transfer to the blender along with the garlic, achiote paste, salt, pepper and vinegar and blend until smooth. Set the marinade aside.

Cut the pork shoulder into 1/4-inch-thick slices and place in a large bowl. Add the marinade and mix well, then cover and refrigerate overnight.

Preheat the oven to 250°F.

Layer half of the bacon on the bottom of a roasting pan. Add all of the marinated pork to the pan and layer the remaining bacon on top. Transfer to the oven and cook until the internal temperature registers 185° to 190°F, about 5 hours.

Cool the pork in the refrigerator for 4 hours, then transfer the meat to a cutting board and slice it as thin as possible. Place all of the meat in a container and refrigerate. Save the remaining fat and juices for the pineapple.

To prepare the pineapple, preheat the oven to 400°F.

Transfer all of the remaining fat and juices surrounding the meat to a saucepan, place over medium heat and heat until liquefied. 

Place the pineapple chunks in a bowl, add the warm meat juices and stir well. Let stand for 5 minutes. Remove the pineapple chunks from the meat juices and place in a single layer on a baking sheet. Transfer to the oven and roast until caramelized, about 40 minutes.

To prepare the empanada dough, in a large bowl, stir together the flour and salt. Add the beef fat and margarine and mix by hand until well incorporated. Slowly add the water and continue mixing until a ball forms, then knead the ball until smooth. Shape the dough into a log, transfer to a sealable plastic bag and let rest for 10 minutes. Cut the dough into 1/2-inch-thick slices, then roll out each slice thinly and cut with a 3-inch round cutter.

Shape each dough round by using your fingers and pinching the dough around the outside of the round and pulling to create a wall around the edges of the open empanada. When finished forming the shells, store in a cool place until you are ready to fill them. 

To prepare the chipotle aioli, in a blender, combine the mayonnaise, lemon juice, chipotle chile and water and blend until smooth. Transfer to a small bowl, cover and refrigerate until ready to serve.

Fill each open empanada three-fourths full of spiced pork. Top with the caramelized pineapple, followed by the cilantro and onion. Drizzle with the chipotle aioli and serve.