It sounds to me like you might be getting out of alignment and dropping your pelvis as you tire. This may be causing your back to arch a bit, which compresses the upper back into the lower back, as your head falls back and your chin starts to point upwards, away from a level neutral position. See where I’m going with this? In addition to leveling your pelvis, make sure you are also lengthening your spine through the crown of your head (think having a ballon attached to the crown of your head). This will open up the back and let the lats relax.
A good trick in your long runs is to set your watch to beep every 10 minutes. When the timer goes off, do a mental body scan and realignment as you run. It only takes getting a little out of alignment to cause discomfort down the road!
Certified Chi Running and Chi Walking Master Instructor