Make the stock: to ensure the pot is large enough to blanch the bones without boiling over, put the bones in the pot and add water to cover by 1 inch. Then remove the bones and set aside.
Bring the water to a boil. When it is at a rolling boil, add the oxtails, beef shank, and pork bones. Return the water to a boil and boil for 3 minutes. Drain the bones into a colander and rinse under cold running water. Rinse the pot and return the rinsed oxtails, neck bones, and shanks to the pot. Add the marrowbones and brisket.
Cut off the pale, fleshy part (the bottom 4 inches) of each lemongrass stalk and discard the leafy tops. Crush the lemongrass with the side of a cleaver or the bottom of a heavy pan and add it to the pot. Add 8 quarts fresh water and bring to a boil over high heat. Lower the heat so the liquid is at a simmer and skim off any scum that rises to the surface.
After 45 minutes, ready an ice-water bath, then check the brisket for doneness by using the chopstick test: transfer the brisket to a plate and poke it with a chopstick; the juices should run clear. If they do not, return the brisket to the pot and continue cooking, checking again in 10 minutes. When the brisket is done, remove it from the pot (reserving the cooking liquid) and immediately submerge it in the ice-water bath, which will stop the cooking and give the meat a firmer texture. When the brisket is completely cool, remove from the water, pat dry, and refrigerate.
Continue to simmer the stock for another 2 hours, skimming as needed to remove any scum that forms on the surface. Remove from the heat and remove and discard the large solids. Strain through a fine-mesh sieve into a large saucepan. Skim most of the fat from the surface of the stock (leave some, as it gives the stock a better flavor and mouthfeel). Return the stock to a simmer over medium heat.
In a spice grinder or mortar and pestle, grind the red pepper flakes and annatto seeds into a coarse powder. In a frying pan, heat the oil over medium heat. Add the ground red pepper flakes and annatto seeds and cook, stirring, for 10 seconds. Add the shallots, garlic, lemongrass, and shrimp paste and cook, stirring, for 2 minutes more, until the mixture is aromatic and the shallots are just beginning to soften.
Add the contents of the frying pan to the simmering stock along with the salt and sugar and simmer for 20 minutes. Taste and adjust the seasoning with salt and sugar.
To ready the garnishes, arrange the basil, perilla, cabbage, lemon and lime wedges, and onion slices on a platter and place on the table. Thinly slice the brisket against the grain. Divide the cooked noodles among warmed soup bowls, then divide the brisket slices evenly among the bowls, placing them on top of the noodles. Ladle the hot stock over the noodles and beef and serve immediately, accompanied with the platter of garnishes.