There are some Cherokee buried at Ft Scott. The name that comes to mind is Deer-in-the-water which is a Cherokee surname. Star Deer-in-the-water, of this family, was killed by Confederate scouts at his home near the Illinois River.
I'm surprised the deserters show up in Confederate units. The recruiters must have been persuasive.
The Cherokee refugees were moved into Missouri to better provide for them. The purpose of the IHG was to get the refugees out of Kansas and to be able to defend themselves once back in Indian Territory. Sturgis hated this plan and threatened to arrest Furnas and Richie, the colonels of the 1st and 2nd, if they didn't stop recruiting.
The 3rd was the Pin Regiment, of course, many of whom were defectors from Drew's 1st Cherokee Mtd Rifles after the Locust Grove affair. The Indian Expedition was headquartered on Flat Rock Creek just north of present Wagoner where these men were "organized" but had to be sent north to be enrolled, armed, and uniformed. Was the 3rd Regt even authorized yet? I'm sure Blunt was all for it but the War Dept initially only authorized two.
I'd like a copy of your transcription too. I can convert it to Word or to a text based pdf for anyone who can't read a MS-Works document.