The way I see it, upper back pain could be caused by you leaning too far forward on the bike, and therefore have to support your torso with your arms more, which translates to using your back muscles as well - muscles between and around your shoulder blades.

If I was having back pain, the last thing I would think to do is get a longer stem lol. I think you should adjust saddle height by very small increments and if you have a trainer, get on the it and see how you feel When I got my bike, I didn't even think of fitting it. I just went home, rode it and adjusted the factors according to what felt bad to me, and eventually found a satisfactory position That may not be the most efficient/accurate way of getting fitted on a bike, but it worked okay for me. By the way, adjusting saddle height is just what I would do if I were in your situation, this is not an expert's opinion by any stretch of the imagination