Combine water and wheat berries in a saucepan; bring to a boil. Cover, reduce heat, and simmer 1 hour or until tender. Drain wheat in a colander over a bowl, reserving 1 cup cooking liquid; set wheat berries aside.
Let reserved cooking liquid stand until warm (100° to 110°). Stir yeast into cooking liquid.
Combine milk, honey, and salt in a small, heavy saucepan, stirring with a whisk until honey and salt dissolve. Heat milk mixture over medium heat until warm (100° to 110°). Add milk mixture to yeast mixture, stirring with a whisk; let stand 5 minutes.
Lightly spoon 3 cups bread flour, whole wheat flour, and amaranth flour into dry measuring cups; level with a knife. Stir 2 1/2 cups bread flour, whole wheat flour, and amaranth flour into yeast mixture.
Turn dough out onto a floured surface. Knead until smooth and elastic (about 10 minutes); add up to 1/2 cup bread flour, 1 tablespoon at a time, to prevent dough from sticking to hands (dough will feel tacky).
Place dough in a large bowl coated with cooking spray, turning to coat top. Cover and let rise in a warm place (85°), free from drafts, 1 hour or until doubled in size. (Press two fingers into dough. If indentation remains, the dough has risen enough.)
Punch dough down; cover and let rest 5 minutes. Coat two 9 x 5-inch loaf pans with cooking spray; dust each with 1 tablespoon bread flour.
Divide dough in half. Working with 1 portion at a time (cover remaining dough to keep from drying), knead half of wheat berries into dough; place dough in prepared pan. Sprinkle dough with 1 tablespoon wheat bran. Repeat procedure with remaining dough, wheat berries, and wheat bran. Cover and let rise 45 minutes or until doubled in size.
Preheat oven to 375°.
Bake at 375° for 45 minutes or until golden. Cool loaves in pans 10 minutes on a wire rack; remove from pans. Cool completely on wire rack.