In a large heavy saucepan bring 3 quarts water to a boil over high heat. Reduce the heat to medium-low, and add the favas and 2 teaspoons of the salt. Cover and simmer until the beans are tender, about 1 1/2 hours. Drain in a colander and rinse under cold running water until cool enough to handle.

To peel the beans, gently pull open the dark end of the skin of each bean with the tip of a small sharp knife or with your fingernail, and peel back the skin. Discard the skins. Put the peeled beans in a bowl.

In a heavy large saucepan heat the olive oil over medium-high heat. Add the bay leaves, crushed red pepper flakes, and the remaining 1 teaspoon salt and heat for 1 minute, stirring occasionally. Add the onions and bell peppers and cook, stirring occasionally, until softened, about 5 minutes. Stir in the parsley and garlic and cook, stirring, until fragrant, about 1 minute. Stir in the tomato paste and 7 1/2 cups water. Bring to a boil over high heat. Reduce the heat to medium-low and simmer until slightly thickened, about 30 minutes.

Add the fava beans and continue simmering until the beans are tender, about 1 hour. Serve immediately, or cool, cover, and refrigerate for up to 3 days.