Rinse beans. In a large pot combine beans and 3 quarts of the water. Bring to boiling; reduce heat. Simmer, covered, for 2 minutes. Remove from heat. Cover and let stand for 1 hour. (Or omit cooking step and soak beans in cold water overnight in a covered pot.) Drain and rinse beans. Return beans to the pot and add 3 quarts fresh water. Bring to boiling; reduce heat. Simmer, covered, for 45 minutes. Drain beans, reserving cooking liquid.
Meanwhile, in a large skillet toast the ancho chiles over medium heat about 5 minutes or until lightly toasted and fragrant, stirring frequently. Let cool. Place peppers in a food processor; cover and process until very finely chopped.
Preheat oven to 325 degrees F. In a 5- to 6-quart pot combine onions, bacon, fresh chiles, and garlic. Cook over medium-high heat about 8 minutes or until onions are tender, stirring frequently. Stir in the drained beans, 4 cups of the bean cooking liquid (add water to make 4 cups if necessary), the ancho chiles, brown sugar, molasses, mustard, salt, and black pepper. Bring to boiling, stirring occasionally. Remove from heat. Cover and bake for 2 hours or just until beans are tender, stirring occasionally and adding water as necessary to maintain a saucy consistency.
Ladle hot beans and sauce into hot clean pint canning jars, leaving a 1-inch headspace. Wipe jar rims; adjust lids and screw bands.
Process filled jars in a pressure canner, at 10 pounds pressure for weighted-gauge canner or 11 pounds pressure for dial-gauge canner, for 65 minutes (start timing when canner reaches 10 or 11 pounds pressure), adjusting for altitude. Allow the pressure to come down naturally. Carefully remove canner lid; cool jars in canner for 10 minutes. Remove jars from canner; cool on wire racks.
To serve, place contents of one jar and 2 to 4 tablespoons water in a small saucepan. Bring to a rapid boil. Boil, covered, for 10 minutes (add 1 additional minute for each additional 1,000 feet of elevation).