Parboil meats and bones in a large pot for 5 minutes, then drain and rinse to remove impurities.
Refill the pot with water and add cleaned bones, beef shank, and pork hocks. Bring to a gentle boil.
Add lemongrass, onion, ginger, and smashed garlic. Reduce heat and simmer 2 to 2 1/2 hours, skimming often.
Warm oil in a small pan. Add annatto seeds and cook until the oil turns deep red; strain out the seeds.
Sauté minced shallot and garlic in the tinted oil, then stir in red pepper flakes and paprika. Set aside.
Lift out the shank and hocks. Cool slightly, slice the shank, and pick hock meat from the bones. Keep warm.
Season broth with fish sauce, brown sugar, and salt. Whisk shrimp paste with hot broth, then strain into the pot.
Stir half the chili oil mixture into the broth. Adjust seasoning with more fish sauce or salt as needed.
Boil noodles until chewy-tender. Rinse under cold water and drain well to prevent sticking.
Assemble bowls with noodles, sliced shank, cha lua, and raw sirloin. Ladle in boiling broth to cook the beef. Top with onions, scallions, herbs, and serve with lime and extra chili oil.