In a large stockpot, parboil the beef bones for 5 minutes to clean them. Transfer them to a bowl of cold water to chill. Wash the bones thoroughly to remove any congealed blood, or other contaminants that can cloud your soup. Drain, rinse, and set aside.
Wash the pot out well, and then, add the boiled beef bones, beef chuck roast, quartered onions, smashed ginger, and 6 quarts water. Bring to a boil, then reduce heat to maintain a simmer (fill the pot with enough water to cover the bones and brisket). Bring to a boil and then lower the heat to a simmer.
Cook for about 2 hours, skimming off any foam or impurities rising to the top.
Now toast the spices (star anise, cloves, cinnamon stick, cardamom pod (if using), fennel seeds, and coriander seeds) in a dry pan over medium low heat for about 3 minutes, until fragrant. To make them easier to remove later, use a kitchen string to tie up the spices in a piece of cheesecloth, before adding them to the broth.
Add fish sauce, sugar, salt, star anise, cloves, and cinnamon stick to the pot.
Continue to simmer for another 2 hours. Skim the surface often to remove any foam and fat.
Taste the broth and adjust seasoning by adding more salt, sugar, and/or fish sauce as needed.
Soak rice noodles in warm water for 20-30 minutes until soft.
Cook the noodles according to the package instructions.Drain and set aside. Prepare the garnishes: thinly slice the onion, chop the green onions, cilantro, and slice jalapeños.Set aside. After the broth has simmered for a total of 4 hours, strain the broth through a fine-mesh sieve into a clean pot. Remove and discard the beef bones, spices, and vegetables.
Remove the beef chuck from the broth, thinly slice it, and set aside.
Bring the broth to a rolling boil.
Assemble the Pho Tai: In serving bowls, layer cooked rice noodles, sliced raw sirloin, and sliced cooked beef chuck.
Pour the boiling hot broth over the top to cook the raw sirloin, make sure the sirloin slices are submerged in the broth.
Garnish the soup with the sliced onions, green onions, cilantro, jalapeños, bean sprouts, and Thai basil.
Squeeze lime wedges over the top.