My right leg is half an inch shorter, and I had problems with my left hip, low-back and leg, as a result of keeping my saddle too low, to accomodate my shorter leg. I have Speedplay pedals, and used a second cleat base (whatever they call the flat part that fits below the cleat), with longer screws, on my shorter leg. I have also moved my longer leg-cleat a little further back, to fine-tune it. With that, along with increasing my saddle height, I have had good results, without doing anything too drastic.