I used to always make bread in the bread machine. It's easy and you can be pretty creative by adding flax and cracked wheat and things. But I never was really happy with the shape of a bread machine loaf. They're tall and boxy, which makes for some REALLY big sandwiches. Plus, we're not very good at cutting nice THIN bread slices, so a bread machine loaf was good for 6 or 8 pieces. 
Then we got the grain mill and started making our own wheat flour. It seemed that it wasn't going to work in the bread machine, the first 4 loaves we made were bricks. What were we doing wrong? So, I started experimenting, looking for answers on the internet, and trying different things. Here is what I've come up with that seems to work pretty well.Mind you, I've adapted this to work for ME and my equipment. I grind my own wheat, and I use the bread machine to knead (because kneading SUUUUUUCKS), but it's possible to do it without these things, you might just have to experiment a little.
Here's my recipe. And I kind of took a little from here and a little from there, and added and took away as I went and made sure to write it down. Bread is pretty easy though, flour, water, sugar and salt, and yeast are all you really need. This recipe uses honey (which I actually prefer when it comes to flavor) and a little oil.
3 cups of lukewarm water
7 cups of whole wheat flour
1 Tbs yeast
1 Tbs salt
1/3 cup Olive Oil
1/3 cup honey
3 Tbs vital wheat gluten
The first thing you want to do is mix everything together. Start with the dry ingredients, then add the honey and olive oil.
Finally add the water. It's important that the water not be too hot or too cold. It's important that it be about 100 degrees to activate the yeast and not kill it. (100 degrees is about the temp of a hot tub) I'm sort of crazy about this.
Then stir it all up until you get a dough ball.
Knead this dough ball for 8-10 minutes. If you don't have a bread machine to put it in, it's important that you knead correctly. (there is a right way and a wrong way to knead bread and it's important to do it the right way or the gluten won't work with the yeast to make the bread rise...who knew, right?) Here's a video explaining how to knead by hand.
Once you've kneaded it, let it rise for about an hour. Again, there's a right way and a wrong way to do this. Since it's still pretty warm outside, I just cover my bowl and set it in the shade outside for an hour. You can also turn your oven on really low and leave the door open a little and set it in there. If your house isn't too cool, you can just set it out on the counter, but the cooler the environment the longer it'll take to rise, so this might take longer than an hour. The way to tell if it's done rising is that it should be double it's original size.
Once your dough is done rising, re-knead it and let it rise for another hour.
Once your dough has risen a second time it's time to shape the loaves. There is also an art to doing this, you don't just lump them into the bread pan.
Flatten out your dough so that it's a rectangle, the short side should be the same length as your bread pan. Then roll it up and place it in the bread pan (make sure your pan is well greased) with the tail of the roll on the bottom. It also helps this process if you put a little olive oil on the counter first. I use a glass cutting board.
Now let it rise one. more. time. I know, it takes forever, that's why you want to make multiple loaves at a time. When your dough has doubled in size, it's ready to put in the oven. Bake for 30-35 minutes, until the internal temperature is 180-200
degrees.
I just use a cheap-o thermometer from the grocery store. But checking the temp is really the best way I've found to make sure your bread is done perfectly.
You'll want to immediately remove it from the baking pans so it doesn't get soggy, and let it sit on a cooling rack with a towel over it until it's cool. I usually let it sit out overnight, then in the morning I freeze one loaf and slice the other one. yum yum yum!!
