Add the achiote paste, sour orange juice, garlic, cumin, oregano, salt, and pepper to a blender. Blend until it turns into a smooth, deep red paste with no lumps. This marinade is what gives cochinita pibil its unmistakable color and tang. Taste it here — it should be bold, since it needs to flavor a lot of meat.
Place your pork chunks in a large bowl or resealable bag and pour the marinade over them, making sure every piece gets coated. Cover and refrigerate for at least 4 hours, though overnight gives the best flavor. The longer it sits, the deeper that citrusy achiote flavor gets into the meat.
Line your pot with banana leaves, add the marinated pork along with all its juices, and fold the leaves over the top to seal it in. Cover with a lid and cook at low heat (around 300°F) for about 3 hours. You'll know it's ready when the meat shreds effortlessly with a fork.
Once cooked, remove the pork from the pot and shred it using two forks, mixing it back with the cooking juices. Those juices are liquid gold, so don't drain them away. The pork should look moist, saucy, and deeply red at this point.
While the pork cooks, blend habaneros, onion, lime juice, and cilantro with a small splash of water until you get a chunky salsa. Adjust the heat by adding more or fewer habanero seeds. This salsa is meant to be fiery, so start small if you're heat-sensitive.
Warm your tortillas in a dry skillet until slightly charred at the edges. Pile on a generous scoop of shredded pork, top with pickled onions, and finish with a spoonful of habanero salsa. Serve immediately while everything is warm and fresh.