I too have MS and currently have pain exactly as you describe. This is the third or fourth time it has happened and each time my GP can find no evidence of infection or irritation. I am 100% convinced that it is MS related but other than paracetamol and ibuprofen I have no way of relieving it.
I don't know much about MS, but I think there is a forum here for MS topics. The kind of pain you're having sounds awful. Very often doctors don't connect things when, in fact, we find out later they are connected. Are you comfortable with your doctor? Can you get a second opinion? What about your primary care doctor? I'm just thinking where you might find other suggestions.