Put whole wheat flour into a 10-inch skillet over medium-low heat. Cook, stirring often with a whisk, until well toasted. This will take about 10 minutes. Flour should be watched carefully to prevent scorching. Set aside.
In a large bowl stir yeast into water to soften. Add brown sugar, oil, wheat bran, soy flour, 1/4 cup wheat germ, and 2 cups unbleached flour. Beat vigorously for 2 minutes. Cover and let rise for 45 minutes. This is a sponge, and will be the consistency of cake batter. The mixture will be frothy and full of bubbles at the end of the rising time. Add toasted flour and salt to the sponge. Beat vigorously until well combined. Gradually add unbleached flour, a little at a time, until you have a dough stiff enough to knead. Turn dough out onto a floured surface. Knead, adding flour as necessary, until you have a smooth, elastic dough.
Put the dough into an oiled bowl, turning once to coat the entire ball of dough with oil. Cover with a towel, and let rise until doubled, about 1 hour. Turn dough out onto a work surface. Divide the dough in half. Shape the dough into loaves. For each loaf sprinkle the work surface with 1 tablespoon of wheat germ. Gently roll the shaped loaf around in the germ so that it becomes lightly imbedded on all sides. Place loaves in well-greased 8 1/2 x 4 1/2-inch loaf pans.
Cover loaves with a towel, and let rise until almost doubled, about 45 minutes. Bake in a preheated 375°F oven for 30 minutes, or until done. Immediately remove bread from pans and cool on a rack.