1. Unless he visited each mess in his regiment and sat down to meals with the men, I don't see how the commander of any regiment in either army could have known each of his men. I graduated from a small college with a graduating class of around 300 with whom I had spent the previous 4 years. We all ate at the same dining hall and the men lived in a total of only 3 dorms, but I doubt that I could name 50 in my class. Most men would know most of the men in their own company, but even the commander would not be expected to know all of the men in all of the companies of a regiment.
2. Quoting directly from Herbert's history of the 8th as published in the Alabama Historical Quarterly in 1977, here is what he had to say about J.S. Spikes: "Spikes, J.S., 8-23-62 – Dale Co,. Ala.: Conscript. Wounded and captured at battle of Gettysburg, 7-3-63. Sent to Fort McHenry Prison, MD. Transferred to Fort Deleware (sic) Prison, Del., n.d. Given wounded parole and sent to hospital at Lynchburg, Va. Received wounded furlough home to Newton, Ala. Paroled at Appomattox C.H., 4-9-65." I don't see anything at all here about him being AWOL, or suggesting that he deserted.
3. The Alabama Department of Archives and History database shows that J.S. Spikes enlisted at Camp Watts, Alabama, which would almost certainly mean that he was conscripted.
Also, concerning Ms. Green. After reviewing all of the cards in the record of J.S. Spikes, it is obvious to me why she stated that there was no Josiah Spikes in the 8th. There is no card in his file that has the name Josiah on it. There is, however, one that clearly states the man's name as James Spikes. Unless having received information to the contrary, that is all she had to go on as to his name and therefore was somewhat justified in relying on that record.
I believe that before one decides to publicly besmirch the good name of anyone, dead or alive, they should have all of their facts in order, and then they should really think hard about whether they should proceed.