Bring a large sauce pot of water to a boil. Add the rice stick noodles and cook until tender, 6 to 8 minutes. Drain and rinse with cold water. Set aside the pot for the soup.
While the rice stick noodles cook, prepare the ingredients for the broth.

• Peel and thinly slice the yellow onion. Divide into two equal portions, one for the broth and one for the soup.
• Cut the lemongrass on the diagonal into ¼-inch-thick slices.
• Tear the lime leaves in several places, keeping the leaves whole.
• Peel and thinly slice the ginger.
• Strip the cilantro leaves from the stems, keeping the stems and leaves separate. Set aside the stems for the broth and the leaves for garnish.

In a medium sauce pot over medium-high heat, combine half the onion with the lemongrass, lime leaves, ginger, cilantro stems, chicken broth, and 3 cups water. Bring to a boil, reduce to a simmer, and cook until the flavors have developed, 10 to 12 minutes.
Set a fine-mesh strainer over the pot used for the rice noodles. Strain the broth into the pot; discard the contents of the strainer.
While the broth simmers, prepare the remaining ingredients.

• Cut the mushrooms into quarters.
• Rinse the shrimp, then drain on a paper-towel-lined plate and pat dry.
• Juice the lime.
• Strip the basil leaves from the stems; coarsely chop the leaves.
• Coarsely chop the cilantro leaves.

To the pot with the strained broth, add the tomatoes, mushrooms, remaining onion, and half the fish sauce. Bring to a boil, reduce to a simmer, and cook, stirring once or twice, until the onion starts to soften, 3 to 5 minutes. Add the shrimp and cook until firm and cooked through, 1 to 2 minutes.
Remove from the heat and stir in 2 tablespoons lime juice. Season to taste with the remaining fish sauce, salt, and pepper.

Transfer the rice stick noodles to individual bowls, ladle the soup on top, and garnish with the basil and cilantro.