Here are the three John F. Shepherds I found in Virginia Confederate Units. I suspect that John of the Goochland Lt. Arty. had just reached the age of 18 subjecting him to Conscription.

John F. Shepherd, Private, Capt. Jonathan Talley's Company (Goochland Light Artillery),* enlisted as Conscript, January 21, 1864 at Richmond by Maj. Peyton for the war, admitted Chimborazo Hospital, Richmond, Va. July 29, 1864, Fever remit (Malaria), furloughed September 6 for 35 days, receipted for an issue of clothing October 28, last recorded present February 28, 1865, no further records

* This company was known at various times as Captain Guy's Company, Captain Talley's Company and 1st Lieutenant Guarrant's Company Virginia Light Artillery; and as the Goochland Light Artillery of Virginia

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John F. Shepherd/Sheapard/Shepperd, Private, (2d) Company C, 36th Regiment Virginia Infantry, enlisted April 12, 1862 at Camp Success for the war, recorded absent without leave March 25, 1863, recorded on June 30, 1863 as sick in hospital at White Sulphur Springs, Va., subsequently recorded as absent, sick at home in Giles County since March, 1863 through October, 1864, captured at Waynesboro, Va. March 2, 1865 and forwarded from Harper's Ferry, West Va., to Fort Delaware, Del. prison March 9, died April 13/14, 1865, Pneumonia, buried on Jersey Shore

The 36th was also known as the 2nd Kanawha
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John F. Shepherd, Private, Company A, 26th Battalion Virginia Infantry, enlisted, conscript, May 31, 1863 at Lewisburg for the war, believe subject to Court Martial August 15, 1864, receipted for an issue of clothing during the 4th Quarter, 1864, subscribed to the Amnesty Oath to the US March 20, 1865 at Charleston, West Va., resident of Greenbrier County, West Va., description: 37 year old Farmer, 5' 6", dark complexion, grey eyes, dark hair

M324: Compiled Service Records of Confederate Soldiers Who Served in Organizations from the State of Virginia