Step 1In a bowl, mix the lime juice, lemon juice, orange juice and grapefruit juice and set aside.
Step 2Cut the pork into 10 to 12 pieces. Rub the pieces lightly with 1 teaspoon salt and set aside in a large plastic-covered bowl.
Step 3In a blender, mix the achiote paste, thyme, 1 teaspoon oregano, garlic, pepper, cumin, paprika and 1 teaspoon salt, and blend with all but 3 tablespoons of the juice (set this aside for pickling the onions). Strain and pour the marinade on the meat. Marinate in the refrigerator, covered with plastic wrap, for at least 4 to 6 hours or, preferably, overnight.
Step 4Heat the oven to 325 degrees. Cover the bottom and sides of a Dutch oven with the banana leaves, overlapping the leaves and letting them spill over the sides of the pot.
Step 5Place the meat in the pot and cover with half the sliced red onion and the bay leaves. Pour in the remaining marinade and cover the pork with a loose portion of the banana leaves. Fold over the banana leaves that spilled over the sides of the pot to wrap the meat. Cover the top of the pot with foil and the lid.
Step 6Place in the oven and cook for 3 to 3 1/2 hours, until the meat is soft. Remove from the oven to let stand covered for another hour or so.
Step 7While the meat is cooking, prepare the citrus-pickled red onions. In a medium mixing bowl, combine the remaining sliced onions with the sliced habaneros. Add the remaining 3 tablespoons mixed citrus juices, the remaining one-fourth teaspoon oregano, one-fourth teaspoon salt and pepper to taste. Let stand for a few hours before using.
Step 8Finely shred the meat with a fork, cover with pan sauces and serve with warm tortillas and pickled onion.