Preheat a dry skillet over medium-high heat. Place the onion halves and ginger slices cut side down and char them until blackened, about 5 minutes. Set aside.
In the same skillet, toast star anise, cloves, cinnamon sticks, coriander seeds, and fennel seeds until fragrant, about 2 minutes. Transfer to a spice bag or cheesecloth and tie securely.
Place the beef chuck roast chunks in the slow cooker. Add the charred onion, ginger, the spice bag, salt, sugar, and water.
Cover and cook on low for 8 hours until the beef is tender and the broth is flavorful.
Remove the beef from the slow cooker and shred or slice thinly. Strain the broth through a fine mesh sieve into a large pot. Discard solids and spice bag.
Stir fish sauce and black pepper into the broth. Keep broth hot on low heat.
Prepare rice noodles according to package instructions. Drain and divide noodles among serving bowls.
Top noodles with shredded beef, bean sprouts, Thai basil, cilantro, green onions, jalapeño slices, and lime wedges.
Ladle hot broth over the bowls. Serve with hoisin and sriracha sauces on the side.