Eek. My sympathies. I have had migraine w/ aura (and also aura w/o migraine) for years (If you have not read it I totally recommend Oliver Sacks' book simply titled "Migraine").
I think that neurological manifestations, be they pain or aura or the movement of energy in the body, are real to the person experiencing them. When I have scotomas, I know YOU can't see them and I know the images are generated within my brain but they are real. When I cut myself, my pain is real.
If you'll permit somewhat of a digression: One of the things I learned decades ago for self-care of migraine, long before taking up aikido, was to "move energy" or chi from my head, deemed in TCM to be too warm, to my hands, deemed to be too cold.
I know of people who learned to to this in a lab setting via biofeedback but I've always been sensitive to my body's internal environment and deviations from the norm, so was able to do it pretty easily by visualization and focus. And yes, a thermometer demonstrated that my hands were having increased bloodflow as the temperature went up.
So when I did start aikido, it wasn't at all hard for me to accept the shorthand of "ki" for the movement of energy within my body. It's not magic, it's learning to use visualization, breath, focus and intent to consciously affect one's autonomic nervous system.
By the way, I also recommend the novel "Lying Awake" by Mark Salzman (yes the guy who wrote the wonderfully funny "Lost in Place" about being a kung fu-besotted kid and "Iron and Silk" about going to China...) - I never expected to enjoy a novel about a nun but it raises very interesting questions. What are the implications when your religious visions may be caused by a neurological problem?