In a large 8-quart stockpot, bring half a pot of water to boil on high heat. Remove any excess fat at the neck or the bottom end of the chicken. Add the chicken to the boiling water and parboil for 5 minutes, transfer the chicken to a large bowl or colander and rinse the chicken, remove any yellow membrane or feathers on the skin or guts inside the chicken.
Clean and refill the stockpot halfway with water and bring to a boil on high heat.
While waiting for the water to boil, preheat a frying pan on medium heat (5 minutes). Peel one onion, trim the root so that it's clean but doesn't fall apart, and cut in half. Dry roast the split piece of ginger and one onion cut in half on all sides in the frying pan (10 minutes). Add the ginger and onion to the pot. Toast the coriander, cloves, and fennel until fragrant (1 minute) and transfer them to a spice ball or make a spice bundle with cheesecloth and string, set aside.
When the water boils, add the chicken back into the pot breast side up, add the sugar, and salt. Add enough water to cover the chicken and still allow 1 inch of room so that broth can simmer without bubbling over.
Lower the temperature to medium heat. After 10 minutes, use a spoon to remove any foam or impurities and discard. Lower the heat to a gentle simmer and continue to cook for 20 minutes.
When the chicken is done cooking, place the chicken (or chicken pieces) into the bowl and when cool enough to touch, debone the chicken, and set aside the deboned chicken in a clean serving plate and cover to keep the meat moist. As time allows, cut the cooked chicken into bite-sized pieces.
Add the chicken bones back into the pot of broth, add the spice ball, and continue to simmer the broth for another 30 minutes.
While the broth simmers, prepare the rice vermicelli according to the package which usually involve soaking in cold water, boiling in water, and finally drain and rinse.
Arrange on a platter with chopped items in separate prep bowls: chop the remaining half an onion, soak in cold water for 10 minutes and drain; chop cilantro; chop scallions; separate the Thai basil so that each person has a sprig; rinse the bean sprouts (optional: parboil in the rice noodle cooking water and drain); slice the jalapeno peppers; cut the lime into 6-8 wedges.
When all the final prep is complete, taste the broth and add more salt as needed, and bring the broth to a full boil. At the same time, assemble the bowls by adding some rice noodles, chicken pieces, bean sprouts, onions, scallions, cilantro, Thai basil leaves, and jalapeno as desired. Add approximately 2 cups of hot broth to cover the noodles and chicken.
Optional: serve with hoisin sauce, fish sauce, and sriracha sauce on the side.