In a large pot, combine the beef shank and brisket with enough water to cover the meat by at least two inches. Bring to a boil over medium-high heat. Reduce heat to low and skim off any foam to ensure a clear broth.
Add bruised lemongrass stalks, quartered onion, fish sauce, sugar, and salt to the pot. Simmer gently for 2 to 3 hours until beef is tender and flavors meld.
Heat annatto seed oil in a small pan over medium heat. Add minced garlic and lemongrass, sauté until fragrant (1-2 minutes). Pour mixture into simmering broth for depth and color.
Cook rice vermicelli noodles according to package instructions. Drain and set aside.
Remove cooked beef from pot and strain broth through a fine-mesh strainer into another pot. Discard solids. Return broth to heat, add chili flakes and adjust seasoning.
Place a portion of cooked noodles in each bowl. Top with slices of cooked beef and ladle hot broth over.
Garnish each bowl with chopped cilantro, sliced green onions, fresh bean sprouts, and Thai basil leaves. Serve with lime wedges. Enjoy!