Rub the fish bones generously with salt and rinse well under cold water.
Add fish bones to a pot and fill with 3 - 4 cups of water. I suggest you use the minimum amount of water to just barely cover the bones to avoid diluting the broth too much. You can always adjust the broth with more water later.
Add 1/2 teaspoon salt and the small piece of ginger to the pot and bring it to a boil. Skim off any foams/scums. When the water starts to boil, reduce heat to low and simmer for 30 - 40 minutes.
Cut tomatoes into wedges.
Slice the fish fillet on an angle to thin slices (about 0.25'' - 0.4''), season to taste with salt and pepper.
After the fish bones have been simmered for 30 - 40 minutes, taste the broth and if you are happy with the flavors, you can discard the bones. Add fish sauce and tomato wedges to the broth.
Prepare dried vermicelli noodles according to instructions.
Lightly dust the fish slices with all purpose flour. Heat a frying pan over medium high heat, when it's hot, add oil and start frying the fish slices until they are cooked through and crispy.
Taste the broth one more time and adjust with fish sauce/water as needed before putting everything together.
In a serving bowl, add noodles, top with fried fish slices and herbs. Ladle the hot soup over the noodles and enjoy. You may squeeze some fresh lime juice and/or add a few slices of bird's-eye chili to your bowl.