Peter,
May I ask what is the "end product" of your current research? Are you doing this because of an ancestor? Are you going to write a book or article? It has been many years now, since I setup my 5th Texas Partisan Rangers "tribute" site. I did it because I had a thought of producing an Indian Territory site including unit histories. I dropped this project, but my cousin Ken Martin, who is a noted Native-American (Cherokee) historian is in the early stages of creating just such a site. If your research doesn't have a home and you'd like to place it on the internet, I'd very much like to include it on my 5th Texas Partisan Rangers site or you might consider getting in touch with Ken.
I hope you'll continue to use this site and the other message boards as a part of your research. I'm really interested to know any info you discover about Martin's Regiment (no relation) and other Indian Territory Civil War history.
Jim