Rinse and pick over the beans. Put them in a large pot with a lid and bring to a boil with the bay leaf and onion. Cover and let boil for 2 minutes. Remove from the heat and let sit for an hour or two to soften the beans.
Seed and stem the dried chilies and toast them for a few minutes in a skillet. Don't burn them. Place in a bowl and pour over the boiling water. Allow to sit and soften for 30 minutes.
Place the red pepper over the open flame on your stove top and rotate every few minutes until it almost completely charred black. Place under a dish towel for a few minutes and then rub off the skin. Cut out the stem/seed and place the pepper into the blender.
Add the chilies and liquid, along with all the spices, salt and cocoa powder. Puree until smooth.
Season the cut up short ribs with salt and pepper. Heat a little oil in a heavy dutch over or other oven safe pot and when very hot, add the short ribs. Allow to brown on one side before stirring. Brown them well and move to a plate.
Reduce the heat a little and add the chopped onion and garlic to the pan. Cook, stirring occasionally, until fragrant. Add the tomato paste to the pan and let it caramelize a little before stirring it in. Add the beer and deglaze the pan. Add the meat, chile puree, tomatoes, beans, and their liquid.
Cover and place in a 325 oven for 3-4 hours until the short ribs are falling apart tender and everything is combined. You can also cook over low heat on the stove top, just make sure in either case to stir every so often and make sure the bottom isn't burning. Add more water if needed if the chili gets too thick.
About 30 minutes before serving, if the chili needs to be a bit thicker, add the crushed tortilla chips and mix in well. Taste and add salt, pepper and lime juice as needed.
Serve with all of the toppings on the side to add while eating.