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 5 1/2- to 6-quart slow cooker, skin-side up (this adds more flavor to the pork and ensures the meat will not dry out). Scatter 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 together in 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 the lime juice, olive oil, oregano, salt and onions together in a medium bowl. Mix well to incorporate. Let stand for 30 minutes. They can be made 1 day ahead.
Serve the pork in the warmed corn tortillas with pickled habaneros and red onions, shredded cabbage and crema.