Place the beef short ribs and knuckle bones in a large stockpot and cover with water. Bring to a boil and cook for 10 minutes. Drain completely, rinse the bones thoroughly, and wash the pot.
While the bones are draining, place the onion, shallot, and ginger on a baking sheet. Broil for 12–15 minutes, turning as needed, until deeply charred.
Toast the star anise, cinnamon sticks, coriander seeds, cloves, and fennel seeds in a dry skillet over medium heat for 1–2 minutes until fragrant.
Return the cleaned bones to the stockpot. Add the charred onion, shallot, ginger, toasted spices, and 13 cups cold water.
Bring just to a boil, then immediately reduce the heat to the lowest possible simmer. The broth should barely bubble.
Simmer uncovered for 5–6 hours, skimming foam and excess fat occasionally. Remove the spice mixture after about 3 hours to prevent the spices from overpowering the broth.
Once the short ribs are fork-tender, about 3½–4 hours into cooking, remove them from the pot and set aside. Continue simmering the broth with the knuckle bones.
Strain the broth through a fine-mesh sieve. For an exceptionally clear broth, strain a second time through cheesecloth.
Return the strained broth to the pot. Stir in the fish sauce, salt, and sugar. Taste and adjust seasoning as needed.
Remove the meat from the short rib bones and shred into bite-sized pieces.
Cook the rice noodles according to package directions. Drain well.
Divide the noodles among serving bowls. Top with shredded short rib meat.
Ladle the hot broth over the noodles and serve immediately with bean sprouts, Thai basil, cilantro, green onions, jalapeños, lime wedges, hoisin sauce, and sriracha.