Combine 1 1/2 cup water, cracked wheat, and salt in a saucepan. Bring to a boil; reduce heat to medium low. Cook, stirring occasionally, until water is absorbed, about 15 minutes. Remove from heat.
Mix 1/3 cup water, sugar, and yeast together in a large bowl. Let stand until yeast forms a creamy foam, about 5 minutes.
Stir buttermilk, honey, molasses, 1/4 cup butter, wheat germ, flax seed, and bran into the cracked wheat until blended. Mix in whole wheat flour.
Mix cracked wheat mixture into the yeast mixture using a spoon or electric mixer. Add all-purpose flour 1 cup at a time, mixing until dough is smooth and elastic.
Place dough in a large greased bowl, cover, and let rise until doubled in size, about 1 hour.
Punch down dough to release air. Divide dough into 2 equal pieces. Roll out pieces into rectangles to release any air bubbles. Roll up, pinching seams tightly and tucking in sides as you go.
Grease two 9x5-inch loaf pans. Place rolls seam side-down in the pans; press down to flatten. Tuck in all sides gently with the top of a finger. Cover and let rise in a warm place until dough rises 1 inch above the rim of the pans, about 45 minutes.
Preheat oven to 375 degrees F (190 degrees C).
Bake loaves until golden brown and the bottoms sound hollow when tapped, about 35 minutes. Brush with 2 tablespoons melted butter and turn out onto wire racks to cool. Allow to cool completely before slicing.