Hey J, I am a longtime yogi and probably have encountered every pain in the body possible that accompanies asanas as they become a diving board to learn more about self care.
It depends what poses you are doing that add to this. Typically it is the shoulderstand and plough that compress the back of the neck. A simple alternative is to place a folded blanket or two under your shoulders so the arc of the cervical curve is maintained when you bring your weight them.
As with chi kung there is always two movements dynamically creating a pose that allows for the grace/yuan chi to emerge. If you find yourself in a pose where you are in a deep one way stretch, ask your body spirit where the energetic counter move is and engage it at the same time.
I have found also that this sort of yin/yanging works well when I am centered from an inner core. For example, in shoulderstand I might allow my awareness to sink into the gravitational center of the pose which is in the throat/head. From a relaxed breath I radiate in all directions from this center and find dynamic interplay and not just a ‘hanging in space’. It is in the hanging where the tendons and ligaments scream.
A wonderful approach that is the closest to our inner alchemy work is the ‘Anusara’ from John Friend. His is a tantric attitude and his understanding of the dynamism of the body’s polarities is right on. You could google it and see if there is anything helpful in his cyber stuff.