I have a few clients with fibromyalgia.  The biggest issue with these clients is neck discomfort when performing mat work with the head lifted.  Of course we modify with the head down, but it seems like we cannot make any gains to strengthen the cervical area without irritating their shoulders and neck.  Any suggestions?

Have you tried working with your clients with the head supported by a cervical pillow?  This gets them closer to the "correct" position without straining the neck and causing  any irritation.  Once they are in teh supported position they can do the exercises and build strength in the muscles surrounding the area.  As they get stronger you can use the pillow less and less, maybe removing it for them for a few reps, until they are strong enough to do it without the additional support.