Do you have forward head posture when standing? Basically, if you stand normally facing forward, are your ears out in front of your shoulders? If so, the extra stress and tension from having to hold your head up may be causing most of your pain. I've had the same issue due to hip problems -- sitting too much caused an 'anterior pelvic tilt', which made my lower back arch forward a bit, which caused my thoracic spine to curve back a bit in an effort to balance out, causing my head to be out in front of my shoulders.
Sadly, lots of people have this issue and don't realize it -- sitting all day, staring down at phones, etc. So, if you find this to be the case (or even if it's not the case), search for ways to fix anterior pelvic tilt and forward head posture. The two main guys I follow are Kelly Starrett (mobilitywod.com) and Naudi Aguilar (functionalpatterns.com). By stretching hip flexors and activating other muscles, you can reverse the issues caused by sitting and bad posture. I'm still working on this issue, myself, so I feel your pain -- literally. I also recommend using something like a Theracane to help loosen up your back and hips even (theracane.com). The Theracane, along with a lacrosse ball and foam roller, will work wonders. Get a foam roller and roll your upper back over it, and it'll feel so great when it helps open it up some.
Also, might be worth seeing a chiropractor. I swear by mine when my upper back is really giving me issues.
Good luck and let me know if you have any questions!