Preheat oven to 400 degrees F (200 C).
Spread stock bones and meat in a large roasting pan. Spray a thin layer of oil onto the bones and meat. Roast on the bottom rack until the bones and meat turn an even golden brown color, about 40 minutes. Flip once, halfway through, and check on the bones frequently. If a higher part of the bones cooks too fast, cover with aluminium foil to avoid burning.
Transfer bones and meat to a large stock pot (I used a 16-quart pot). Pour a cup of hot water into the roasting pan and scrape the brown bits off the pan. Pour everything into the stock pot.
Add cold water to the stock pot to cover the ingredients by one inch. Turn on high heat. Add green onion, ginger, bay leaves, Japanese sake, and aromatics to the pot. Cook until bringing to a boil, stir a few times, and turn to low heat. Cook the broth at a gentle simmer. Cover and cook for 4 to 6 hours (remove the beef during this process), until the all the collagen on the bones has fallen off and the marrow is mostly dissolved. During the cooking, check on the stock and skim the brown foam from the top with a large spoon.
(Option 1) If you’re going to make beef stew - After 1 hour of simmering, remove the beef chuck from the pot and transfer it to a container to use later.
(Option 2) If you’re going to serve the beef immediately - Remove the beef when tender, after 2 to 3 hours.
When the stock is ready, you can remove the bones and turn to high heat to reduce the soup so it’ll be easier to store.
Drain the stock with a colander and transfer it into airtight containers. Do not skim the fat from the top. You can store the stock in the fridge for 1 week or in the freezer up to 3 months.