In a very large (9- to 10-quart) Dutch oven (you'll use it for braising the meat), roast the garlic cloves over medium heat, turning from time to time, until soft and blackened in spots, 10 to 15 minutes. While the garlic is roasting, roast the chiles over an open flame or 4 inches below a preheated broiler, turning regularly, until the blistered and blackened in spots. Let the garlic cool until handleable, then peel and roughly chop. Cut a slit in the side of each chile.
Turn the oven on to 325 degrees. Set the Dutch oven over medium-high heat and film with the oil. Sprinkle the meat with salt, lay in the hot oil and sear all sides to a rich golden brown - this will take about 10 minutes. Transfer to a plate.
With the pot still over medium-high, pour in the tomatoes, along with the roasted garlic, red onion, green pepper, black pepper, oregano and epazote (if you're using it). Cook until the mixture starts to thicken, about 10 minutes. Meanwhile, mash the achiote paste and vinegar together until smooth.
When the sauce has reduced, stir in the achiote mixture and enough water (usually about 2 cups) to bring the depth to about 3/4-inch. Taste and season with salt, usually about 1 teaspoon. Nestle the meat and whole roasted chiles into the sauce, cover the pot and slide into the middle of the oven. Cook until the meat is so tender that it's nearly falling apart, about 2 hours.
Mix together the chopped green onion with the habanero. Moisten it with a little fresh lime juice and season with salt.
Transfer the short ribs to deep serving plates (pasta bowls work well here). Spoon off the fat that has risen to the top of the sauce. Taste and season with more salt, if you think necessary. Spoon the brothy sauce over the short ribs, topping each serving with one of the banana peppers. Serve right away, passing the salpicon separately for each person to use al gusto.