Place 2 cups whole wheat flour and yeast in a large bowl. Set aside.
In a small saucepan, combine molasses, butter, water and salt and heat on low just until butter melts (120-130 degrees).
Add warm mixture to flour and yeast. Beat with electric mixer on low for 30 seconds, scraping the bowl. Then beat on high for 3 minutes.
Gradually add the seeds and the rye flour, using the electric mixer. Add as much of the remaining whole wheat flour as you can stir in with a spoon. Move dough to a floured surface and knead in the remaining flour.
Place dough in an oiled bowl, turning once to coat with oil. Set in a warm place to rise until double (60-90 minutes).
Punch down dough. Divide in half and shape into two loaves. Place on a baking sheet and let rise until double (45-60 minutes).