Curious CSR. Shortly after being captured at Spotsylvania, Jonathan Allred applied to join U.S. service and did so at Point Lookout MD. I don't see a definite match with a US CSR. However, he's present on the August 1864 rolls and listed as a deserter on the October 1864. Next he's paroled at Lynchburg VA, Apr. 13, 1865, as a member of Co. "A", 2nd Florida Regt. Finally, he signs a parole at Salibury NC, July 6, 1865, as a resident of Rowan County NC.

As a match for a census record, Jonathan Allred's age when enlisted at Pensacola FL is given as 26. He appears to match Jonathan Allred, age 24, a grocer living in Montgomery AL. I don't see any other census or military record matches for this name.

Here's a MA Thesis on the 2nd Florida Regiment. I've not read it, but would bet this regiment never passed through Alabama --
http://etd.lib.fsu.edu/theses_1/available/etd-07112005-175844/unrestricted/Thesis.pdf