I saw the flag in question when I was at Wilson's Creek a little over a year ago. When I came home I did some digging into it a well and was also not coming up to the conclusion that the flag belonged to Stand Watie's regiment.
I am swamped with some things that have to get done soon so I don't have the time to really dig into this but if you give me your address I will be happy to copy my Indian flag files and send them to you to see if you can come up with something for this. From what you have just sent you are way ahead of me on this curve anyway.
Please email me directly at Biggsg@charter.net
Greg Biggs