For the pulled pork: Heat the vegetable oil in a medium saucepan over medium-high heat. Add the onions and cook until translucent, about 4 minutes. Add the garlic and cook until fragrant and slightly softened, about 2 more minutes. Add the achiote paste and mix well to incorporate. Add the orange and pineapple juices and bring to a boil. Once it boils, turn the heat off and carefully transfer to a blender. Cool. Process the mixture until smooth, about 2 minutes. Set aside.
Sprinkle the pork butt heavily with salt and pepper on all sides. Arrange the orange skins on the bottom of a slow cooker, skin-side up (this adds more flavor to the pork and ensures the meat will not dry out). Place the pork butt on top of the oranges. Pour the achiote puree inside the slow cooker. Cover the slow cooker and turn on to high heat. Let it cook until the pork is tender and ready to shred, about 5 hours.
Turn the slow cooker off and remove the oranges from the pot and discard. Let the pork cool slightly before shredding. Using two forks or with clean hands, shred the pork. Return the shredded meat to the slow cooker filled with sauce and keep warm until ready to serve.
For the pickled habaneros: Mix the habanero chiles, lime juice, olive oil, oregano and salt into a small bowl. Mix well to incorporate. Let stand at least 20 minutes. They can be made 1 day ahead.
For the pickled red onions: Mix together the red onions, lime juice, olive oil, regano and salt into a medium bowl. Mix well to incorporate. Let stand for 30 minutes. They can be made 1 day ahead.
For the fried black bean filled tortillas (panuchos): Using a 5-inch round cookie cutter, cut a smaller tortilla out of each tortilla. Save the scraps for making chilaquiles, tortilla soup, etc. Heat 2 tablespoons of vegetable oil in a medium saute pan over medium-high heat. Then add the beans to warm and soften, about 5 minutes, stirring continuously to avoid burning. Turn the heat off and reserve.
In a large saute pan, heat the remaining 1/2 cup of vegetable oil to 350 degrees F. While the oil is heating, form the panuchos. Start by spreading 1 tablespoon of warmed beans on the surface of the tortilla. Stack the second tortilla over it pressing on the edges to seal. Remove the excess beans on the side of the panucho. Working in batches, fry the panuchos until golden in color, about 3 minutes per side. Remove from the pan and drain on a paper-towel-lined plate.
To serve: Top each panucho with about 1/3 cup of cochinita pibil. Top with the pickled red onions and habaneros, if desired. Take a bite, die and go to heaven.