In a large stockpot, bring 5 quarts water to a boil. In a second pot, add bone marrow, beef chuck, and water to cover. Bring to a boil and cook for 5 minutes (to get rid of all impurities). Using tongs, transfer the meat and bones into the first pot of boiling water. Bring to a boil, reduce heat to simmer, and skim off fat.
Add ginger, onion, fish sauce, and sugar. Simmer for 2 hours. Wrap star anise and cloves in cheesecloth, tie with kitchen twine, and place in broth. Allow to infuse until broth is fragrant, about 30 minutes more.
Over a fine-meshed sieve lined with cheesecloth, strain broth into a bowl. Submerge bowl in an ice bath and cool. (If broth is not clear, strain again with a fresh piece of cheesecloth.) Season with salt and pepper.
To serve, divide noodles and beef slices among 4 bowls. Bring broth to a vigorous boil and ladle into bowls. Garnish with scallions, bean sprouts, basil leaves, chile, and lime.
It's important to get it as clear as possible to avoid a greasy taste and texture, which is why you start it in one pot and transfer it to another. For best results, make it the day before, refrigerate overnight, and skim the fat off the top before reheating.