Pour boiling water over farro and quinoa in a small bowl. Let stand for 10 minutes.
Combine 2 cups whole wheat flour, spelt flour, yeast, vital wheat gluten and salt in a large mixer bowl. Heat milk, water, honey and oil to very warm (120° to 130°F). Add milk mixture to flour mixture. Beat for 3 minutes until almost smooth. Beat in remaining 1 cup whole wheat flour, farro mixture, flax seeds and chia seeds. Add enough all-purpose flour to make a soft dough. Knead on lightly floured surface until smooth and elastic, about 6 to 8 minutes. Cover and let rest for 10 minutes.
Divide dough in two equal portions. Form into round loaves and place on separate baking sheets that have been sprayed with cooking spray. Or place in two greased 9 x 5-inch loaf pans. Cover and let rise until double, 45 to 60 minutes.
Preheat oven to 350°F.
Bake bread for 45 to 55 minutes, until well browned. (If using 2 baking sheets, switch between oven racks half way through baking.)
Let cool on racks or in pans 5 minutes, then turn out on wire racks to cool completely.
Recipe Note: If spelt flour is not available use an additional 1/2 cup whole wheat flour.