So, here's the recipe I use for baking bread. Using freshly ground flour will make the loaf denser, so I compensate some by adding extra liquid and yeast. This is the recipe for using bread flour.
Two pound loaf:
1 1/2 cups buttermilk at 80˚ (1 TBL cultured buttermilk added for each 1/4 c water)
1/4 cup oil
1/4 cup honey
2 tsp salt
1/2 tsp baking soda
4 TBL wheat germ
4 1/4 cups flour (usually end up adding an additional 3-4 TBL more)
4 tsp wheat gluten
1 1/4 tsp yeast
I put the ingredients in the bread machine in that order and let it run the entire mix/knead cycle (about an hour and a half). Then I take it out and form it and let is rise for a little over an hour, and then bake it on 350˚ for half an hour. About halfway through the baking I lay a sheet of foil over it so the crust doesn't brown too much. I've found that for forming the dough, using a little oil rather than flour to make it not stick to the counter will help the dough not get too dry. In my experience, drier dough doesn't rise as well.
For making it with the mixer rather than bread machine, I mix the ingredients for about 10 minutes, let it rest for an hour and then punch it down before I shape it.
For the freshly ground flour, I use 1/3 cup oil and honey (if you use the same measuring cup for the honey that you used for the oil, the honey just falls right out). I'll add a little more baking soda and use a little over a tablespoon of yeast. I also leave out the wheat germ, since it hasn't been taken out of the flour.
In both cases, I will substitute about 1/2-3/4 cup of the flour for ground up flax. I just pour some into the 1 cup measurer and top it off with flour.