To make the broth: In a large pot, combine the water, shallots, shiitake mushrooms, garlic, carrots, ginger, peppercorns, cloves, brown sugar, soy sauce, rice vinegar, and 1/2 bunch cilantro. Bring to a boil, reduce to simmer, cover, and simmer for 1 hour. Strain the broth and discard the solids. Keep the broth simmering until ready to use.
Cook the rice noodles according to package directions.
Divide the noodles between 4 bowls. Top with the scallions, basil, mushrooms, carrots, and baby bok choy.
Pour the hot broth over each bowl. Serve with lime wedges, remaining cilantro, and extra soy sauce.