In a large heavy-bottomed pot or Dutch Oven, combine the beans, bay leaves and 2 quarts (8 cups) of water. Bring to a boil, over medium high heat, then lower the heat to a simmer and cook until the beans are tender, about 1 hour.
Using a colander set over a bowl, drain the beans, collecting the broth into the bowl. Add chicken stock to complete 6 cups of liquid. Reserve the broth and the beans.
Wipe down the pot and bring it back to the stove, over medium heat. Heat the olive oil and sauté the pancetta until golden brown. Remove and place in a paper towel-lined plate to soak up the excess grease. Reserve.
Add the onion, leek, carrot and celery, sautéing until softened, about 5 minutes. Then, stir in the minced garlic and cook for a minute or two, or until fragrant.
Stir in the thyme leaves and cook for about a minute.
Add the pancetta back into the pot. Then, add the crushed tomatoes, tomato paste, parmesan rind, reserved broth, salt and pepper.
Cover, lower the heat to medium-low and simmer for 10 to 15 minutes.
In the meantime, cook the pasta separately, according to package instructions.
Add reserved beans and cooked pasta to the soup.
Stir in the grated parmesan cheese. Taste for seasoning and adjust salt and pepper.
Stir in the sliced basil, reserving some for garnishing.
Garnish with basil and fresh thyme. Serve immediately.