If he was in the 54th or the 37th, they had both been in some horrendous battles. However, this is a man's honor we are discussing. All these years later, I, personally am not willing to hang the term "deserter" around his neck. Even though I think his actions were reasonable, I am not sure he would feel the same. Each and every time he made application for his pension, he was granted it, as was his second wife, Abbie. Those men had ample opportunity to question him, and it is apparent to me that some were in the 37th Mississippi.
I think your analogy of the school records is a good one, but what if there really were an Alan J. Pettus? I have found a Matthew R. Barnes marrying a Marinda Ann Sauls in Dekalb, AL on Dec. 18, 1851, and another Matthew R. Barnes on the 1880 Georgia census. These are not the same man. So, there were at least two men with that name living and of an age to have been in the Civil War.
Is it reasonable to assume that a war department clerk put the two jackets together as one. I do not know if they are two men or one man. I have ordered his service record which I will examine....if all of it is his. You have put a lot of time into this discussion, and I appreciate all you have told me. Your knowledge is astounding. I also know you can be much more dispassionate about this than can I. I am not related; my husband is. But I have been researching his family for over 30 years. Mathew is our brick wall. We do not know where he came from, or who his parents were. There are about four or five of us who are still searching.
Thanks you so much for your input.