Tear the chilies in half and discard the ribs and seeds. Bring a large pot of water to a boil. Add the chilies and simmer for about 10 minutes, pushing the chilies down from time to time, until they begin to break apart.
Remove 1/4 cup of the pepper water. Drain the peppers.
Put the cumin seeds, coriander seeds, cloves and cinnamon in small skillet. Toast over medium heat, swirling the pan from time to time until they begin to smoke and have a fragrant aroma. Transfer to a plate to cool. Add the oregano to the spices.
Put the garlic and spices in the jug of a powerful blender. Add the pepper water, cider vinegar and orange juice, then the chilies. Blend, scraping down the sides of the jug as needed until fairly smooth.
Sprinkle the trimmed short ribs generously with the salt. Put the short ribs on a parchment lined baking sheet, meat side up. Spread about 1/2 of the rub over the top and sides of the short ribs. Reserve the remaining rub.
Lightly cover the meat with plastic wrap and refrigerate for 1 day.
The following day, preheat the oven to 350˚F.
Cut the onions into large chunks and place in a mixing bowl. Add the remaining marinade and a generous pinch of salt.
Remove the core from the tomatoes and slice them lengthwise. Lay the tomatoes on the bottom of a roasting pan, cut side down.
Add the bay leaves and garlic cloves and pour in the chicken stock. The chicken stock should reach about 3/4 of the way up the ingredients in the pan. Add more chicken stock or water if needed.
Place the short ribs over the vegetables. Cover the roaster with parchment and then foil. Seal the foil tightly around the pan.
Place into the oven and cook for 1 hour.
Turn the oven down to 300˚F and continue to cook for another 4 hours.
Remove the foil and parchment. The meat should be very soft and tender. If it is not, re-cover and continue to cook, checking it every 30 minutes.
Ladle some of the cooking liquid from the bottom of the pan (to avoid the surface fat) and pour over the meat. Continue to cook uncovered for 1 more hour.
Remove the roaster from the oven and turn the oven off. Carefully move the short ribs to a parchment lined baking sheet, tent with foil and return to the oven to keep warm.
To make the salsa, use a large, slotted spoon or spider to transfer the vegetables (discarding the bay leaves) to the jug of a blender. Blend until smooth and season to taste with salt. If you prefer a spicier salsa, blend in jalapeno peppers to taste.
Strain the remaining liquid into a saucepan. Ladle off the clear fat that rises to the top and discard. Bring to a boil and reduce for 15 minutes or longer for a more intense flavor. Season with salt to taste.
To serve, pull the meat from the bones and shred into bite-size pieces. Spoon some of the reduced liquid in the bottom of each serving bowl. Top with the meat and spoon some of the salsa around the top.
Garnish with the onions and a squeeze of lime.