All I have on your ancestor was in some notes from a researcher, in Company K, 12th MO Cavalry Regiment (CSA) a Private B. L. Pemberton of Saline County, surrendered at Shreveport, Louisiana on 14 June 1865. I mostly do irregular (bushwhacker) stuff and not this regular Confederate work, so I am out of my comfort zone on this, but this note does put a Benjamin Pemberton in the correct regiment and matches a Benjamin Pemberton who would have entered service late in the war.
I couldn't find anything on him in the online Missouri Secretary of State, Missouri State Archives records. No service record. These Confederate records are not complete, lots of holes or missing records.
I looked in the 1860 census of Marshall Township, Saline County in HeritageQuest, and think I found Benjamin in the Thomas and Mrs. Sarah Pemberton family, both 45, both born in Virginia. Thomas had $6,000 in real property and $6,000 in personal property. He would need it since I counted eleven children from age 3 up to age 18. All of the children born in MO. Here they are in order, Elizabeth 18, William 15, Benjamin 13, Sarah 12, David 11, Silas 8, Edward 7, Laura 7 (I think), Walter 6, Preston 5, Dolly 3.
If I did my math right, this Benjamin would have been born about 1847, which is not 12/26/1844. I would guess that, if this is the same Benjamin as the one in 12th MO Cav, he could have joined Company K in about 1862, and more likely 1863, 1864, or 1865 as a teenager, who MAY have fudged on his age to get accepted in the unit. Kids in those days put a lot of store about not lying, so Benjamin might have put a piece of paper in his shoe and told the recruiter he "was over 16" if 16 was written on the paper in his shoe. That way he was not telling a lie in a literal sense. There were other stunts teenagers used to avoid telling an actual lie about their true age, but, of course, these were mind games to the kid, and still misrepresentations.
That's about all I can do, but there is a strong chance the Marshall TWP Benjamin Pemberton is your man (er, kid). Does having your Benjamin Pemberton coming from near Marshall, county seat of the large Saline County fit any part of what you have already?