My theory for that mysterious first verse:

In April, 1861, the "Magnolia Regiment" was organized at Fort Morgan, Alabama. This regiment served as the Fort Morgan garrison until March, 1862, when it was ordered to Fort Pillow, Tennessee. Here it was disbanded because its term of service had expired.

Now, the Magnolia regiment was also known as the 2nd Infantry Regiment, or 2nd Alabama, OR POSSIBLY -- wait for it -- 2nd 'Bama. It's not hard to imagine the soldiers sitting around their campfires in February or March of '62, waiting for the end of service, singing "ain't gonna be in the 2nd 'Bama long …"

… and this fragment was eventually picked up by Andrew and Jim Baxter and recorded in 1927.