From the index to compiled service records, it seems clear he is either John Walton (D), or John F Walters (B). I will have to get their compiled service records to determine which (and may not be able to even then).
He was born in 1827/28. [source: date: 2 (33 in 1861)]
When he enlisted, he was living in Philadelphia, Pennsylvania. [source: 2]
He enlisted and was mustered into service, at Philadelphia, Pennsylvania, on 14 October 1861. He was mustered in as a private, in company B. [sources: 1, 2]
He was not on the muster-out roll when the regiment mustered out. [sources: 1, 2]
1 Bates, Samuel Penniman. History of Pennsylvania volunteers, 1861-5. Harrisburg: B. Singerly, state printer, 1869-71. 5 volumes. 'Ninety-first regiment', volume 3, pages 186-233. (In the roster)
2 Civil War Veterans' Card File, available at the Pennsylvania State Archives, searched 29 June 2004 (John Walton)