Remove 2 Tbsp of lemongrass and set aside in a small bowl. Combine the remaining lemongrass, shallot, garlic, soy sauce, sugar, fish sauce, chili flakes and salt in a large bowl. Add the chicken and turn to coat, tucking some marinade underneath the skin. Pour any excess marinade into the bird cavity. Cover the chicken with plastic wrap, then marinate in the refrigerator for at least 4 hours, preferably overnight. Bring the chicken to room temperature before baking.
Preheat the oven to 350˚F. Put the chicken, breast side down, on a rack in a roasting pan. Bake for 40 minutes. Turn the bird over and roast until the chicken is cooked and nicely browned, about 20 to 30 minutes more. About 10 minutes before the chicken is done, combine the remaining 2 Tbsp lemongrass with the cilantro and oil. Brush the mixture on the bird, then continue to roast until it is done and the juices run clear. Let the chicken rest 10 minutes before carving. Serve with Soy-Lime Dipping Sauce and fried or steamed rice. (The pan juices are delicious on the rice).
Place the garlic, chilies and sugar in a mortar and pound into a paste. (You can also chop the garlic and chilies by hand.) Transfer to a small bowl and add the soy sauce, lime juice and water. Stir until well blended. This sauce will keep up to 3 weeks if stored in the refrigerator in a tight-lidded jar.