Add boiling water to a pot large enough to fit in the chicken. Add a pinch of salt and chicken to the pot. Let it boil for a minute, then remove the chicken and discard the liquid.
In a pan over medium heat, dry roast the ginger and shallots until fragrant and lightly develop colors. Set ginger and shallots aside.
Reduce the heat to medium low. Add cassia bark/cinnamon, star anises, coriander seeds and black cardamom pod (if using) and toast just until fragrant. Be careful not to let them burn. Put spices in a spice pouch.
In a clean pot, add chicken, ginger, shallots, spice pouch, 2 teaspoons of salt and 9 cups of water. When it starts to boil, skim off any foams and lower heat to a gentle simmer.
Cover and simmer for 15-20 minutes or until the chicken is just cooked through. You can test by using a meat thermometer, or inserting a chopstick and see if the juice runs clear. Remove the chicken from the stock pot.
Put the chicken in an ice bath to stop the cooking. Then take it out of the ice bath, separate the meat from the bones. Add the bones back to the pot. Continue to simmer the broth for at least 45-60 minutes, or more until flavors are concentrated to your liking.
Before serving, taste the broth and flavor with 2-3 tablespoons of fish sauce to taste.
Pressure Cooker Method
Add 1 piece of ginger and half the shallots with the chicken to your pressure cooker. Add 2 teaspoons of salt and 6 cups of water. Close the lid and valve, pressure cook on High for 3-4 minutes (depending on the size of the chicken).
Slowly release the pressure manually. Remove the chicken from the pressure cooker, put it in an ice bath to stop the cooking. Then take it out of the ice bath, separate the meat from the bones. Add the bones back to the pressure cooker.
Add the remaining ginger, shallots and the spice pouch to the pressure cooker. Pressure cook on High for 20-30 minutes (the longer the better), and let it release pressure naturally.
Once pressure cooking is over, taste the broth and see if you can add some more boiling water without diluting the flavors. Before serving, flavor with fish sauce to taste.
While the broth is cooking, shred or slice the chicken into bite-sized pieces. Prepare pho rice noodles according to package instructions.
Separate the white and green parts of the scallions. Thinly slice the green parts while quickly poach the white parts in the broth. Also slice the onion very thinly.
Add pho rice noodles to serving bowls, top with chicken meat, scallions and thinly sliced onions. Top with freshly cracked pepper. Bring the broth back to a boil and then ladle broth into serving bowls.
Serve immediately with birds-eye chili and lime wedges on the side.
If you have extra chicken bones, add them to the broth for even stronger flavors.