Well, the fact that this is a sharp, intermittent pain, in the same location, which comes and goes -- makes it seem that a nerve in the scalp is being irritated.
Such specific nerve irritations would cause a sharp, well defined pain (in contrast to more headache syndromes, which would be a more diffuse, longer lasting dull ache in most cases, or the sharp eye icepick as in cluster).
I would think that the nerve itself is inflammed, causing these sudden sharp pains.
You are correct in that this is difficult to diagnose, since there isn't a test that really diagnoses these types of pains. It is good you had the imaging tests and other tests to rule out other potential issues, but perhaps if this continues to go on, your doctor or a pain doctor can perform an injection (a nerve block - which would be some numbing medication and steroids) right in that area -- and if the pain is relieved, then you've got your diagnosis.