Plump (soak) the raisins in ¼ cups of the milk for 30 minutes. Drain, reserving the milk. Combine the yeast, whole wheat flour, and remaining I cup milk. Let stand for 30 minutes until very foamy. Meanwhile, bring 2 cups water to a boil in a small saucepan. Add the quinoa and amaranth and simmer, uncovered, until the grains are tender, about 10 minutes. Remove from heat and let stand covered until the water is completely absorbed, 10 minutes; cool.
Combine the bread flour, spelt flour, brown sugar, and salt in a mixing bowl. Add the yeast mixture and ½ cup of the raisin-plumping milk; knead for 30 seconds. Add the quinoa, amaranth, raisins, and walnuts; knead until the dough comes together and forms a slightly tacky ball of dough, adding additional plumping milk as needed. Knead for 6 minutes by hand, sprinkling with bread flour if the dough becomes too sticky.
Transfer the dough to a greased mixing bowl; turn to coat with oil. Cover with plastic wrap; allow to rise in a warm place for 1 hour, until nearly doubled. Turn out onto an unfloured work surface. Punch down the dough and divide it in half. Grease two 8½ x 4½-inch loaf pans; shape the dough into two loaves and place in the pans. Cover with greased plastic wrap; allow to rise for 2 hours, until more than doubled. When the dough has almost finished rising, heat the oven to 350°F.
Bake in a 350°F oven for 50 to 60 minutes, until golden brown and internal temperature reaches 190°F. Test by knocking on the loaf—it should sound hollow. Cool on racks.