--improvement in symptoms with increasing gabapentin dose wouldn't indicate a possible cause or location of the neuropathy; gabapentin is not only used for peripheral symptoms but for spinal nerve root (radiculopathy) pain/parastheses, as well as for treatment of seizures, its original indication. And certainly it is a good thing if it helps keep your symptoms in check.

And, yes, the gold standard for determination of small fiber neuropathy, at least currently, is a skin biopsy to evaluate and enumerate small, unmyelinated fibers that subsume the sensations of pain and temperature.

The fact that the report says you have peroneal nerve damage must mean that some disruption of signal was found in that nerve distribution, but that is a large, myelinated fiber finding, as EMG and nerve conduction studies cannot measure the very tiny unmyelinated nerves. It's certainly possible that is a symptom cause--although no one is exempted from being co-morbid--having more than one cause contributing to symptoms. I, for example, have both small-fiber problems and cervical spine nerve root compression that I am trying to avoid surgery for, and both contribute to my upper body symptoms, particularly in my right hand.