Make the Bitter Orange Juice: Mix the lime and orange juices in a large bowl.
Make the achiote marinade: Measure the dry ingredients in a spice grinder and pulverize. Transfer to a blender jar and add the garlic, salt, and vinegar. Blend until completely smooth. Allow mixture to sit in refrigerator for 4 hours or overnight.
Preparing the Chicken: Preheat an oven to 350 degrees.
Place chicken thighs in a large glass (non-reactive) baking dish. Add the citrus juice to the marinade and pour over the top and allow it to sit for at least 4 hours.
Roast the chiles over an open flame or close up under a preheated broiler, turning regularly until the skin is blackened and blistered all over, about 4 minutes for an open flame, 6 minutes for a broiler. Cool, then pull off the stems, slice the chiles in half lengthwise, gently scrape out the seeds, then flip the chiles over and scrape off the charred skin. Slice the cleaned chile pieces crosswise into ¼-inch strips. Slice the tomatoes into 12 round slices.
Heat a medium 10 inch skillet over medium heat and film with oil. Add the onion and cook until golden and softened, about 10 minutes. Combine the onion and chiles.
Cut the banana leaves into 12 inch squares (you will need at least 12) with no tears or holes. Warm the leaves over an open flame to soften. Layer a few banana leaves and place 2 chicken thighs in the center. Top with 2 slices of tomato and a portion of the onion-chile mixture. Sprinkle with salt. Fold the banana leaves and tie with butchers twine or thinly ripped pieces of banana leaf.
Place on baking sheets with a rim in case anything leaks. Bake for 45 minutes. Unfold Leaves. Serve with pickled red onions.