Rinse the beans in cold water, picking them over to make sure they are clean. Place the beans in a large bowl and cover with water. Soak them for 8 to 12 hours or overnight.
Discard the water, and rinse the beans again. Place them in a 3-quart saucepan, and cover with fresh water. Add the 1 chopped onion and 2 cloves minced garlic, cover, and bring to a boil over medium heat. Cook until the beans are tender, stirring occasionally but gently to keep the beans intact, 45 to 60 minutes. Drain in a colander and cool the beans by gently rinsing them under cool water. Transfer the beans to a large heat proof mixing bowl.
While the beans are cooling, prepare the mushrooms. Preheat the broiler. Clean each mushroom, and pat dry. Sprinkle all with 2 tablespoons of oil. Broil the mushrooms until tender, about 5 minutes. Remove from the oven, and set aside.
Heat the remaining 2/3 cup of olive oil in a 9 inch skillet. Add the minced onion, parsley, bell pepper and remaining 1 clove minced garlic. Cook, stirring for 1 to 2 minutes and then season with salt to taste. Remove from the heat and cool slightly.
Pour over the cooled beans. Stir and toss lightly so that the seasoning coats the beans evenly. Spoon over the cooked mushrooms.