In a large stockpot, bring 6 quarts water to a boil. Place the bones and beef chuck in a second pot and add water to cover. Bring to a boil and boil vigorously for 5 minutes. Using tongs, carefully transfer the bones and beef to the first pot of boiling water. Discard the water in which the meat cooked (this cleans the bones and meat and reduces the impurities that can cloud the broth). When the water returns to a boil, reduce the heat to a simmer. Skim the surface often to remove any foam and fat. Add the charred ginger and onions, fish sauce and sugar. Simmer until the beef chuck is tender, about 40 minutes. Remove 1 piece and submerge in cool water for 10 minutes to prevent the meat from darkening and drying out. Drain, then cut into thin slices, and set aside. Let the other piece of beef chuck continue to cook in the simmering broth.
When the broth has been simmering for about 1 1/2 hours total, wrap the star anise and cloves in a spice bag or piece of cheesecloth and add to the broth. Let infuse until the broth is fragrant about 30 minutes. Remove and discard both the spice bag and onions. Add the salt and continue to simmer, skimming as necessary, until ready to assemble the dish. The broth needs to cook for at least 2 hours. (The broth will taste salty but will be balanced once the noodles and accompaniments are added.) Leave the remaining chuck and bones to simmer in the pot while you assemble the bowls.
To serve, place the cooked noodles in preheated bowls. (If the noodles are not hot, reheat them in a microwave or dip them briefly in boiling water to prevent them cooling down the soup.) Place a few slices of the beef chuck and the raw sirloin on the noodles. Bring the broth to a rolling boil; ladle about 2 to 3 cups into each bowl. The broth will cook the raw beef instantly. Garnish with yellow onions, scallions, and cilantro. Serve immediately, inviting guests to garnish the bowls with bean sprouts, herbs, chiles, lime juice, and black pepper.