You might be able to find a copy of Benet's "Treatise on Military Law" (1862) -- I downloaded it once but can't seem to find a url now. There's also Kautz's COS for officers, which has a lot on court martial proceedings. The two volumes of General Orders of the War Department covering '61-'63 have examples of reports on significant courts martial.
All of that will give you a lot to work with, but you may be trying to do too much with one form. For example, the "arrest warrant" may in this case may be one special order, with another for setting the time and place of the trial, which in turn will require you to draw up and present the accused with charges and specifications.