Is there a numbering scheme for this highway system? What's the highest number?
I think it depends on the reservation. The Navajo Nation had a very extensive road network but not every tribe in the Four Corners Region emulated the Signed Highway convention. I've never seen a Bureau of Indian Affairs (BIA Route) in California.
The Navajo Nation has a DOT site: https://www.navajodot.org/; maps with route numbers (https://www.navajodot.org/Maps_.aspx); and a log of priority routes (https://www.navajodot.org/uploads/files/Appendix%20F%20Priority%20Routes%2003082016.pdf)