My conclusions:
1) Cochran’s 1864 company was a Provisional Enrolled Militia unit, despite the fact that it was known as Cochran’s Company C Six-Month Enrolled Missouri Militia.
2) The reason that some 70 men of the approx. 120 men who enrolled in his unit were simultaneously enrolled in Company A of the 79th Regiment E.M.M. was simply to meet a requirement in Special Order No. 89 that each regiment in the 3rd Military District have a company of especially reliable men that could be called upon if necessary.
3) That the company ceased to be Company A of the 79th Regiment after Special Order No. 89 was revoked by Special Order No. 90 on Aug. 29, 1864.
4) That Cochran’s 1864 company—whatever it was called—was active “full-time,” as opposed to the early E.M.M. units that were active only a few days at a time when they were ordered to respond to emergencies.
5) That Cochran’s 1864 company was—except for the aforementioned affiliation with the 79th Regiment—an independent unit, despite being known as “Company C.”
Despite my last conclusion I would imagine there was a superior officer that Cochran could have at least turned to for advice. In an earlier post, Kirby Ross speculated that he could have reported to a colonel in the 79th regiment. But I wonder if that would be so if Special Order No. 90 repealed any relationship Cochran's company might have had with the 79th Regiment at the end of August 1864.
In the Provost Marshal's database, I did find a letter that Cochran wrote to a superior officer in December 1864. Unfortunately, it is addressed only to "Col." I've copied it below, deciphering Cochran's handwriting as best I could, in the case that it might provide you, Mr. Ross, or anyone else clues. My own feeling is that it would have made more sense for Cochran to be coordinating with a regiment in Cape.
George Williams
Post Dallas, Mo., Dec. 11, 1864
Col.,
I have made inquiry concerning the man Aldred that was killed in this county sometime in the summer and I find that this same Jesse Alred was a guerilla harborer and a guerilla himself and that his son William is a guerilla and was with a band of guerillas a few days since in this settlement and robbed some union citizens, and I also learned that Mrs. Jesse Alred went to the Cape and got powder and caps and contrived to get them through the pickets by placing them under her dress in the pocket of an inside dress.
Col., there are some families in the McGee Settlement that I think ought to be (worked??) on. They are the Neal family, Cato family and two McGee families. They harbor and feed the guerillas and their Negroes do their milking and drive their stock for them, and they have driven off Union men's hogs 10 and 12 in a lot. They have hog pens in the woods where they get their meat. One of the McGee Negroes does some of the worst robbing that is done. I would like to move those families from that settlement if it can be done without going contrary to military regulations. The Cato men and a man named Barnhart (?) and some others came within three miles of this Post a few nights since and killed a man named Joseph Mynes, a good Union man. They set him down on the ground and made him sit straight and one of them stood on his legs and held him as another man held a candle to his nose and burned it until they were satisfied with their barbarous way of treating him and they then shot him. I think their families should be removed from the settlement. Our boys are getting so enraged at these proceedings that I think if there is not something done to stop them, there will be bad work done. The citizens are all preparing to leave the county on account of the guerillas and their families.
I am your obt. servant,
John R. Cochran,
Capt., Company C 6 Mo. E.M.M.
Post Dallas, Mo.