Pour boiling water over shredded wheat cereal in a large mixing bowl. Stir in the salt, molasses, and butter; let cool to about 100 degrees F (40 degrees C), about 15 minutes. Grease two 9x5 inch loaf pans.
Sprinkle the yeast over the 1/2 cup of warm water in a small bowl. The water should be no more than 100 degrees F (40 degrees C). Let stand for 5 minutes until the yeast softens and begins to form a creamy foam.
Stir the yeast mixture into the cooled cereal mixture. Beat in the whole wheat flour, rye flour, and flax seed. Beat in the all-purpose flour. Turn the dough out onto a lightly floured surface and knead until smooth and elastic but not stiff, about 10 minutes.
Lightly oil a large bowl, then place the dough in the bowl and turn to coat with oil. Cover with a light cloth and let rise in a warm place (80 to 95 degrees F (27 to 35 degrees C)) until doubled in volume, about 1 hour.
Deflate the dough and turn it out onto a lightly floured surface. Use a knife to divide the dough into two equal pieces. Form the dough into 2 loaves, and place the loaves into the prepared pans. Cover with a damp cloth and let rise until doubled in volume, about 30 minutes.
Meanwhile, preheat oven to 325 degrees F (165 degrees C).
Bake in the preheated oven until the top is golden brown and the bottom of the loaf sounds hollow when tapped, about 50 minutes.