Hi Joel,
I too have severe back pain, but in my lower back due to some herniated discs. Mine has mostly subsided since I started bicycling regularly (4-6 rides a week). I find that if I keep with a regular regimen of workouts the pain stays away, and if I take a hiatus, the pain returns, especially if I take a few weeks off. I have also had issues with pain when adjusting my bicycling position, even the tiniest bit. Just a stem change will send me into weeks of discomfort until my body adjusts to the new position, which can be quite frustrating. For you, not having yet found the perfect position, I would highly recommend a professional bike fit. I've had very good results @ Bike Doctor in Frederick. They should be able to account for the type of pain that you are experiencing into the bike fit to help address the situation. Best of luck to ya, don't get discouraged, there is a perfect position. You just need to find it!