Lyme and its coinfections are just so baffling. A lot of times neck and shoulder pain are caused by tight muscles. Have you tried magnesium? I swear by it as every time I would go to the doctor with stiff neck, aching back, she always told me to take magnesium (one time I even got a shot) and it helps tremendously. Lyme strips the body of magnesium and it is a crucial mineral for our muscles.
It could be your lyme nodes are swollen with is common with lyme and co-inf. Make sure you drink a lot of water with lemon and try epsom salt bath and it could be your body is not detoxifying correctly and unable to get rid of the toxins.
Have you ever read this article? It is very helpful.
http://www.benbrew.com/lb/lyme5.pdf
Hope you feel better today.