I recently added to the sidebar historical journals that had a fair amount of interesting Civil War content [Or at least I thought they all did--I looked through the 'previous issues' page of the Journal of South Texas and found only one CW-related article. It looked very good, however, so I ILL'd it.] and wanted to mention which ones actually had full articles available to view online or download.
Kansas Historical Quarterly has their articles transcribed (not scanned) and presented in a very eye pleasing format.
Kansas History also has some articles online.
The Chronicles of Oklahoma has many articles dealing with the Civil War in the Indian Territory. So far only volumes 1-20 are available. They are also transcribed, but I am not sure yet how much Civil War content is in these 1921-1942 volumes.
Pdf files of back issues of Ohio Valley History are available. There is an interesting article by Brian McKnight about Humphrey Marshall in there (see vol. 5, no. 3), kind of an introduction to his book Contested Borderland.
West Virginia History has the text from volumes published from 1990-97 online.