If you look on Google at the southwest side of the Muskogee Airport where the line comes in from Leonard, there is another one that heads southwest toward Wainright, Hichita, Dewar and into Henryetta. I was able to follow it to Dustin, and then lost it southwest of Lamar.
I think you are following the Missouri Oklahoma & Gulf, later the Kansas Oklahoma and Gulf RR.
http://www.trainweb.org/screamingeagle/history_ko&g.htmlIt served: Denison, TX, Carpenter's Bluff, TX, Achille, OK, Durant, OK, Tupelo, OK, Calvin, OK, Henryetta, Ok, Council Hill, OK, Muskogee, OK, Wagoner, OK, Miami, OK, and Baxter Springs, KS.
If you go north out of Wagoner and then towards Locust Grove, you can trace a lot of what appears to be the old ROW, including some bridge piers across the river.
There was also another track that departed Muskogee west of Hatbox Field going to Okmulgee. I haven't been able to follow any of them through Muskogee.