Using a colander or a large sieve, drain the soaked wheatberries. Return them to the saucepan with fresh water to cover. Bring to a boil, lower the heat, cover, and simmer for about an hour, until tender.
In a separate pot, add 2 cups of water, bring to a boil and add the rice. Cover tightly, and bring down to a simmer. Simmer for 45 minutes then turn off the heat and let stand for 15 minutes.
While the grains cook, saute the onions and garlic in the oil in a large, skillet on low heat for about 10 minutes, until golden. Stir occasionally to prevent sticking. Add the mushrooms, thyme, rosemary, and soy sauce and cook for 5 minutes. Pour in the wine and continue to simmer until the wine evaporates. Set aside.
When the wheatberries are soft, drain any excess liquid and then add to the sauteed mushrooms. Stir in the cooked rice, mix thoroughly, and serve immediately.