This dough can rise in Brotformen -- German baskets that mold the loaves. The grains are available at health food stores.
Bring a small saucepan of water to a boil. Add wheat berries, and gently boil for 20 minutes. Drain, and let cool. In the bowl of an electric mixer, combine 1/4 warm cup water, yeast, and honey. Let stand until yeast is foamy, about 10 minutes. Add sponge, and mix on low speed until combined, about 1 minute. Add flours, rye meal, cracked wheat, millet, flax, salt, and remaining 2 1/4 cups warm water; mix, using the paddle attachment, on low speed for 2 minutes. Change to dough hook, and mix on medium-low speed for 6 minutes. Add sunflower seeds and cooked wheat berries; mix for 1 minute. Pull dough down from the hook, and press the dough into the seeds at the bottom of bowl. Continue to mix until the seeds are completely incorporated and the dough is wet and tacky, 2 minutes. Alternatively, knead the dough by hand, 15 to 20 minutes.
Transfer to a lightly floured surface, and knead by hand, four or five turns, into a ball. Place the dough, smooth side up, in a lightly oiled bowl, and cover with plastic wrap. Let rise in a warm place until increased to 1 1/2 times the size, about 2 1/2 hours.
Punch down dough, and fold it over onto itself four or five times. Turn folded side face down in the bowl. Cover, and let rise in a warm place until doubled in bulk, 1 hour.
Liberally sprinkle two braided Brotformen, if using, with flour. Turn dough onto a lightly floured surface, and cut in half. Cover one piece of dough loosely with oiled plastic wrap. On an unfloured surface, knead the other piece of dough into a ball. Cup your hands around it, and move it on the work surface in small, circular motions, until top is rounded and bottom is smooth.
Place the shaped loaf, bottom up, in a Brotform. Cover loosely with lightly oiled plastic wrap and then with a towel. Repeat shaping process with the second piece of dough. (If you're not using Brotformen, shape dough in the same way, and place on parchment dusted with coarse cornmeal; coat the bottom and 1 inch up the sides with cornmeal. Cover loosely with oiled plastic wrap and then with a clean towel.) Let loaves rise in a warm place until doubled in bulk, about 1 hour. Thirty minutes before this final rise is completed, place a baking stone, if using, in lower third of oven and an empty baking pan on the lowest shelf. Heat oven to 450 degrees.
Transfer one loaf from a Brotform to a baker's peel or baking sheet sprinkled with coarse cornmeal. Using a razor blade or serrated knife, slash the top 1/4 to 1/2 inch deep. Slide onto the baking stone. Repeat with second loaf. If not using a stone, slash tops and bake on a cornmeal-dusted baking sheet. Quickly pour 2 cups of very hot water into the heated baking pan to create steam, and close the oven door. Bake until dark golden brown and hollow sounding when tapped on the bottom, about 25 to 30 minutes. If the bread darkens too quickly, lower temperature to 425 degrees after 15 minutes of the baking time. Let bread cool on a wire rack for at least 30 minutes before slicing.