The MS Hug can cause many types of pain. Your shoulder/scapula pain sounds similar to one of my ribcage attacks (MS Hug). I woke up one morning screaming in agony truly believing ribs had broken during my sleep with one end of one rib poking through my breast and the other end of another rib poking through my scapula. After several weeks, the attack remitted about 50%. If you haven't yet had a thoracic MRI, I suggest you ask for one which might show correlating lesions.
To help with this pain, I get Lidocaine intercostal muscle (the muscles between the ribs) trigger point injections all over my scapula area and other areas which last for four to six weeks. I'll be trying Botox in the injections next month to see if it works better and longer than the Lidocaine injections. My MS specialist gives me the injections, but many pain management doctors will also give them.
Another idea is to use prescription Lidoderm 5% pain patches as needed during flares--trust me, they DO help. They saved me during the worst of my MS Hug attacks and flares. Up to three patches can be worn at one time, and doctors easily prescribe them because the medication does not go through the blood stream so does not cause stomach, liver, nor kidney damage; is not addictive; and has virtually no side effects nor negative interactions with other meds. Ask your primary doc to prescribe them; you may not even need to see your doctor if he or she will call in the prescription directly to your pharmacy.
Best of luck.