He can be located on the 1860 census. John J. and Caroline Allen farmed not far from Court Hill in Talladega County. That's closer to Lineville than Ashland, which became a post office in 1866. The town name for Lineville came from being located along the antebellum county line. Clay County did not exist at this time, and Lineville is nowhere near a county line today.

As mentioned, several men named John J. Allen lived in Alabama in 1860. Due to your ancestor's age and family (age 40 in 1862), it seems unlikely that he would have enlisted until required to do so by law. An enlistment for a man named John J. Allen was recorded in neighboring Calhoun County on Oct. 28, 1864. As a conscript, he was assigned to Co. "A", 12th Alabama Regiment. By the time he arrived in Virginia, the 12th Alabama would have just returned to Richmond after a long and costly campaign in the Shenandoah Valley. The record shows that he was captured during the retreat to Appomattox and sent to prison at Point Lookout MD. After his release on June 7, 1865, Allen was released to go home.