I've experimented with a lot of whole wheat bread recipes and this one turns out really good for me each time. I do use a stoneware bread pan to bake it in, and that probably makes a lot of the difference.
1 cup water
3 TBS honey
1/2 cup unbleached white flour
2 1/2 cups wheat flour (white or red wheat)
1 1/2 TBS powdered milk
3 TBS Gluten flour (can buy this in the health food section or bulk bins)
1 TBS flax seed (optional--also in health food or bulk bins)
1 1/2 tsp. salt
2 TBS butter (I use real)
2 tsp yeast
Load in machine. Run through dough cycle. Punch down. Shape into loaf. Let rise about 35 minutes. Bake at 350º for about 35 min. Loaf should sound hollow on the bottom when turned out of pan. I like to rub butter on the top of it to make a softer crust.
The water might need to be altered depending on your altitude. I would load it, and get it mixing good. If it is a bit dry add a little water til the dough is sticky to the touch without sticking to your finger.
I also bought a dough enhancer from Emergency Essentials. I'm not sure where else you can get that, but I have been adding a Tablespoon of that.