For the soup: Heat the oil in a heavy large pot over medium heat. Add the onion and ginger and sauté until the onion begins to soften, about 5 minutes. Add the broth, 2 cups water, fish sauce, and sugar. Place the star anise and cloves in a tea ball or wrap in cheesecloth and add to the pot. Or, if using ground allspice, simple add it to the pot and eliminate the cloves. Bring to a boil. Add the chicken and return to a boil. Reduce the heat and simmer until the chicken is tender, about 20 minutes.
Meanwhile, place the noodles in a large bowl. Cover with boiling water and let soak until almost tender, at least 10 minutes. Let the noodles stand in the water until ready to use.
For the condiments: Place the jalapeno in a small bowl, place the bean sprouts, basil leaves and lime on a platter. Prepare the remaining condiments.
Using tongs or a slotted spoon, remove the chicken from the pot. Add the shiitake and bok choy to the pot and simmer until beginning to soften, about 5 minutes. Season the broth to taste with salt. Slice the chicken crosswise.
Drain the noodles and divide among 4 large bowls. Divide the chicken among the bowls. Ladle the broth and cooked vegetables over the noodles and chicken. Sprinkle each bowl with green onions, cilantro, and freshly ground black pepper.
Serve the pho steaming hot, allowing diners to season to taste with hoisin, chile paste, lime juice, and jalapenos, and then to heap on bean sprouts and fresh basil leaves.