Vance,
In Annie Abel's 'The American Indian in the Civil War, 1862-1865' are several references to the Shawnee and Kiowa. I consider Abel's works the most scholarly works on the subject as they are based on considerable primary source material of the Indian Office as well as the Official Records and in many cases included the entire text of correspondence in the footnotes. The entire text of this book is online at several places including Google Books.

There were three main groups of Shawnee and apparently many "wandering" bands. Today, the Absentee Shawnee are headquarter in Shawnee OK, the Eastern Shawnee in Seneca MO & West Seneca OK, and the Shawnee Nation in Miami OK. I believe the Absentee Shawnee are those who along with Cherokee and Delaware migrated to the Cape Girardeau MO area and ultimately to Texas (and Mexico) and then into Indian Territory. There were two towns on the south side of the Canadian just upstream of the mouth of Little River called Shawneetown. (There is also a Shawneetown on the north side of the Red River near the Arkansas border). Some of the Texas Cherokee settled at Cherokeetown near Ft Arbuckle -- one of my ancestors, George Fields, brother of Chief Richard Fields of the Texas Cherokee, was living here with his son Dempsey after the Cherokee were driven from Texas. Texas Cherokee also relocated to Texanna OK and what is now "Duchess Creek" was originally Dutch's Creek, Dutch being a leader of this group. But I digress ;-)

Abel references a couple of reports in the ORs by Albert Pike which mention the Kiowa being "friendly" to the South and, as I recall, they are mentioned with the Comanche.

Abel also references correspondence of the Union Indian Office in Kansas which mentions Shawnee and Kiowa and many other tribes and bands and efforts of the Indian Office to keep them 'friendly'. It seems all was in confusion and these loosely organized tribes became many disconnected bands. The nature of the culture of the Plains Tribes was a rather loose confederacy anyway. The eastern tribes had formerly had more centralized government but decades of warfare, dislocation, etc had made them essentially refugees and they became very fractured. I'm reminded of a speech by the Chickamagua Cherokee leader Dragging Canoe in the late 1700s that begins with the question "Where now are our Grandfathers the Delaware?" referring to how the once great tribe so respected by the Cherokee had been shatterred and scatterred by years of contact and conflict with the colonists and European powers. The Shawnee had a similar fate in the Ohio Valley.