Hi Agnes, if you take away the Little Big Horn studies, there's not a lot of archaeological research on Indian War sites of the late 1800s. For the southern Plains, you might want to look into Jerome Greene's and Doug Scott's work on the Sand Creek Massacre site in SE Colorado (1864), and J. Brett Cruse's research on Red River War sites in Oklahoma and Texas (1874). Not sure, though, to what extent these may help with your specific interest. Still, I hope you find something of use in them, Michael
Also of interest to you may be the NPS investigations into the site of the Lodge Pole (Washita) massacre (27 November 1868). See, for instance, William B. Lees et al., Archaeology of the Washita Battlefield National Historic Site (Oklahoma Historical Society, 1997).
Michael, thanks again for your suggestions, including the War Horses of Bar-sur-Aube. I'm sure there must be more literature available. Thus, it is a very interesting work in progress. Have a great day!