Pick over and rinse beans. Put them into a large bowl and cover completely with cold water. Let the beans soak overnight (or for at least 8 hours). Or use the quicker method described in "Soaking Dried Beans". 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 in the rice and chicken stock in a medium saucepan. Bring to a boil over medium-high heat. Cover, reduce 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.