Preheat oven to 350°F.

Place onion, ginger, and chicken bones in a roasting pan and roast for 1 hour, moving the vegetables and bones around in the pan after about 30 minutes. . Remove from oven and let the onion and ginger cool.

Peel the onion and cut it in half. Slice the unpeeled ginger into thin slices (no need to peel).

Place the onion, ginger, bones, water, salt, and brown sugar in a large stock pot.

Bring the water to a boil and then lower the heat and simmer for 3 hours, adding another quart (4 cups) of water if needed (the water line should remain about 1 inch above the bones).

Use a large slotted spoon to remove most of the bones and chunks of onion from the stock. Then, strain the stock through a fine-mesh sieve into a heatproof bowl or pot. Cover and let chill for at least one hour, or, overnight (preferred). Remove the lid and use a spoon to skim most of the congealed fat from the surface of the stock.

In a medium saucepan, add enough oil to come up less than ⅓" up the pan (about ¼" is enough). Heat the oil over medium-high until it registers 340°F on a deep-fry thermometer.

Carefully add the shallots to the hot oil and fry them, stirring, until light golden brown, about 4 to 6 minutes (watch closely, don't let them burn!)

Using a slotted spoon, transfer the shallots to a paper towel-lined plate to drain. Set aside.

Bring a large pot of water to a boil over high heat.

Add the chicken, scallions, ginger, and salt and boil for 15 minutes, then turn off the heat, cover the pot, and let stand for 25 minutes.

Just before the chicken is ready, prepare an ice-water bath in a large bowl.

When the chicken is done, carefully use tongs and a large spoon to remove it from the pot and immediately submerge it in the ice-water bath, which will stop the cooking and give the meat a firmer texture. Discard the cooking liquid, or store (chill or freeze) it for another use.

Let the chicken chill for about 20 minutes, or until the chicken is cool enough to handle easily, remove from the water, and pat dry.

Pull the chicken meat from the bones, discarding the bones and skin. Shred the meat with your fingers; you should have about 4 cups (this step can be done a day ahead).

In a large saucepan, bring the stock to a simmer over medium-high heat. Taste and add more salt (or fish sauce) until you reach the correct balance of seasoning.

Prepare the rice noodles according to package directions and distribute them evenly among soup bowls.

Prep the garnishes and arrange the basil, bean sprouts, lime wedges, jalapeños, and fried shallots on a platter and place them on the table.

Top each serving with about ¾ cup of the shredded chicken, then divide the scallions and cilantro evenly among the bowls.

Ladle the hot stock over the top, dividing it evenly, and sprinkle with the fried shallots.

Serve at once, accompanied with the platter of garnishes.