I recently revisited the one issue I own of Savas Publishing's Journal of the Indian Wars. Volume One-Number 3 [see Table of Contents from Savas-Beatie website] deals with the Civil War years. In addition to the fine articles, there is a recommended reading section. The essay is attached to a lengthy article by Michael Hughes that comprehensively covers the Civil War-era conflicts with various Indian groups. I've been searching for a good book that details Kit Carson's Navajo campaign.
Of course, Carson is a highly divisive figure and a book that one person would judge simply as fair, others might find extremely negative or fawningly positive. Perhaps an example of this phenomenon would be Hughes' essay comment on Kit Carson: Indian Fighter or Indian Killer?, deeming it "a hard-nosed examination" of Carson. This is in sharp contrast to this professor's review of the same work, that found it to be a rather useless pro-Carson polemic. I think I'll start with Trafzer's The Kit Carson Campaign: The Last Great Navajo War. It's been characterized as a very harsh attack on Carson's historical reputation (and thus drawing fire from later books), so I am surprised Hughes' essay gives the opposite impression. In light of the contradictions above and the fact that Hughes has the author of Clifford E. Trafzer's book as E.O. Clifford, I am thinking that the essay was written hastily from memory. On the other hand, the other recommendations seem to be in line with current opinion and I found the list to be useful overall. I guess I'll find out for myself. That's the best way anyway.
The Journal of the Indian Wars was sadly short-lived as a quarterly publication, and I would greatly recommend getting a copy of this issue while it is still available new. While not directly Civil War related, I found Volume 1-Number 2 Battles and Leaders East of the Mississippi to be very interesting as well.