Place onion halves and ginger slices cut-side down directly on a gas burner or under a broiler for 3-4 minutes until charred dark brown. Let cool slightly, then rinse off any loose black bits under cool water; set aside.
In a dry skillet over medium heat, toast star anise, cinnamon stick, coriander seeds, fennel seeds, and cloves for 1-2 minutes until fragrant. Transfer to a spice bag or cheesecloth tied with kitchen twine.
In a large pot, add chicken thighs and cover with cold water. Bring to a boil over high heat and cook for 3 minutes. Dump out the water, rinse chicken and pot to remove impurities for a clear broth.
Return chicken to the clean pot, add 10 cups cold water, charred onion, ginger, spice bag, fish sauce, rock sugar, and salt. Bring to a gentle simmer over medium heat, then reduce to low. Partially cover and simmer until chicken reaches an internal temperature of 165°F (74°C), about 30-40 minutes, skimming any foam occasionally.
Once chicken registers 165°F (74°C), remove thighs with tongs. Allow to cool slightly, then pull meat from bones, discarding skin and bones. Shred meat into bite-size pieces; keep warm.
Strain the broth through a fine-mesh sieve into a clean pot, discarding solids. Taste and adjust with more fish sauce or salt if needed. Keep hot over low heat.
Cook rice noodles according to package directions until just tender, then drain and rinse under warm water. Divide among 4 large serving bowls.
Top noodles with shredded chicken, then ladle simmering broth over until ingredients are submerged. Serve immediately with a platter of bean sprouts, Thai basil, cilantro, lime wedges, jalapeños, green onions, and hoisin/sriracha on the side.