I've been making my own sourdough for about two or three years now and I've gotten down making a good one that works in bread machines at this point. My personal recipe is as follows:
1/2 Cup Sourdough Starter
3 Cups Bread Flour (Not all purpose, that will give you a bowling ball)
1 Cup Graham Flour
1 1/4 Cups water
2 Teaspoons Salt
1/4 Cup Flax Seeds (Optional)
If you don't know how to make Sourdough Starter I'll go over that soon. Put your starter and water in the bottom of the bread pan. Give it a stir or two with a wooden spoon to mix the yeast and water a bit. Add the flour next, then the salt and seeds if you want those in it.
Run the bread machine on the "dough" cycle. Run it about three times in a row to get the gluten properly stretched out. Note this is why you can't make bread with all purpose flour: it doesn't have enough gluten. All purpose flour is for things like muffins or banana bread, things that are crumbly instead of stretchy like sourdough bread. If you have a food processor with a dough hook, use that instead of a bread machine, it will work better. This saves you all the stretching and kneading serious sourdough fanatics have to do.
After three doughcycles in the bread machine, transfer the lump of dough to a floured proofing basket. Rice flour works best but you can use all purpose flour to coat the basket just fine. Put it in the oven with the oven light on and leave it about six to eight hours. This is a tricky bit because you're not working on exact time schedules, you're using wild natural yeast and every town's yeast is a bit different. You just have to check it periodically to see how it's going.
Once it's risen take it out and put a dutch oven inside your oven. Heat it to 450 degrees and leave it for half an hour. Put the loaf out of the proofing basket and onto a sheet of parchment baking paper, then transfer it to the oven. Slash the top with a groove, a lot of bakers get fancy with complex patterns but I generally just put an X on it myself. Before putting the bread in the oven, you can baste the top with olive oil, or sprinkle some sesame or poppy seeds on it, there's a few ways to dress it up if you like.
Bake it with the lid on about half an hour. Turn the temperature down to 400 degrees and bake it with the lid off for another half an hour. Put it on a wire rack to cool and don't cut it until it's fully cooled, the inside is still cooking during this stage.