Thank you again for your help. I've been able to compile a fair amount after I determined where he was. Jones is a fairly hard name to trace if you have no historical background to begin with.
A remaining mystery is Henry and Annie's oldest son, Jeremiah (or Jerry). He was about 17 or so in 1864. I haven't found him in the 1864 census of men available for duty (or whatever it was called) so I wonder if he was killed during the War as well. He is not with the Joneses in Union County in 1870 or near them with his own family.
That's not as high on the list but still an unsolved mystery.