trying to get the hang of making good artisan bread, and my last loaf tasted great. But it stayed flatter than previous efforts, and was very tough.  I am doing my best to understand the science as clearly as possible, so I want to know what part of my process I should look at tweaking to get the results I want? 
Toughness is usually the result of either too much gluten (which in turn comes from using a flour too high in protein), or not enough fat (or possibly adding the fat at the wrong time).  Poor volume on the other hand is usually the result of using low-protein flour, and thus not having enough gluten formation.  Therefore it is logical to assume that the most likely cause of your bread troubles is the fat. Try adding some more fat. 