In answer to the Captain/Colonel question:

According to this obit from a KY paper, he was made a staff officer with the rank of Captain.
Sorry, I have been under the weather for a while, and don't have it in me to transcribe it. I don't understand the reference to Nov 1865.

http://chroniclingamerica.loc.gov/lccn/sn86069395/1912-02-08/ed-1/seq-8/#date1=1912&index=4&rows=20&words=Clark+H+M&searchType=basic&sequence=0&state=&date2=1912&proxtext=%22M.+H.+Clark%22&y=11&x=14&dateFilterType=yearRange&page=1