Drain the beans and transfer them to a large pot. Add the 3 cups water. Bring to a boil over medium heat and cook for 5 minutes. Stir in the onion, garlic, oregano, and bay leaf. Reduce the heat to low and simmer, uncovered, for about 1 hour, until the beans are tender. Add the chili powder, cumin, coriander, red pepper flakes, and tomato juice, stirring to mix. Continue to cook while preparing the rice. Put the rice and chicken stock in a medium saucepan. Bring to a boil over medium-high heat. Cover, reduce the heat to low, and simmer for 45 minutes, or until tender. In the meantime, combine all the salsa ingredients in a small serving bowl and set it aside for the flavors to meld. When the rice is done, stir it into the bean mixture. Ladle into bowls and serve with the salsa on the side.