Your information about Benjamin F. Jolly and Joseph M. Jolly is very well thought out and carefully composed. Only one problem. You may notice on Benjamin's record in Company A, 52nd EMM in the remarks section that it says he "Enlisted in Regular service." It seems both Benjamin and Joseph joined Company A, 33rd Missouri Infantry (Union) just a few days apart in August 1862. Joseph's record in the 33rd says he "Died June 15, 63 of disease at Helena, Ark." and Benjamin's says "Died Feb. 13, 65 in Hosp. St. Louis, MO" and "Buried Jefferson Barracks near St. Louis MO." Therefore, it had to have been another Jolly killed in north Morgan County during the war.
Regarding Cotty or Cody or whatever, I did find two separate records of a James Cody of Versailles, Morgan County, or of Moniteau County with one write-up in the southern Missouri State Guard and another record presumably of the same James Cody in Company F, 5th Missouri Infantry (Confederate). He was in several campaigns through Vicksburg, then he disappeared from the southern army in September 1863.
Your discovery of Humphrey Cathey of Morgan County living near a Joseph Jolly family seems promising. I did not think to look for that spelling. The detail you discovered seems to fit very well.
Thanks, John
Bruce Nichols