Makes 2 round loaves
Heat 2 cups water, molasses, vinegar, butter and chocolate in heavy small saucepan over low heat until butter and chocolate melt, stirring frequently. Cool to 105 F to 115 F.
Sprinkle yeast and sugar over warm water in small bowl; stir to dissolve. Let stand until foamy, 10 minutes.
Mix all-purpose, rye and whole wheat flours in medium bowl. Measure 2 cups flour mixture into large bowl of heavy electric mixer fitted with paddle. Add bran, caraway, salt, coffee, shallot and fennel. Blend in vinegar and yeast mixtures on low speed until smooth. Increase speed to medium and mix 5 minutes to develop gluten. Decrease speed to low and stir in enough remaining flour mixture 1/2 cup at a time to form dough that pulls away from sides of bowl. Knead dough on floured surface until just smooth and elastic, about 3 minutes, kneading in additional all-purpose flour if very stick; dough will be slightly tacky.
Grease large bowl. Add dough, turning to coat entire surface. cover bowl with plastic. Let rise in warm draft-free area until doubled, about 1 hour.
Sprinkle 2 baking sheets with cornmeal. Gently knead dough on lightly floured surface until deflated. Cut in half. Knead each piece into round. Place on prepared sheets. cover with waxed paper or towel. Let rise until doubled in volume, about 45 minutes.
Preheat oven to 350 F. Slash X into of loaves, using serrated knife. Bake until well browned and loaves sound hollow when tapped on bottom, abut 50 minutes. Immediately transfer to racks. Cool completely before slicing.