Jim:

The Union court martial records are in the National Archives in D.C. Thomas and Beverly Lowry have within the past year come out with a CD index of these records, and do lookups for a fee.

The records of Confederate court martials are rarely, if ever, in their CSRs. Certainly I've never seen one, and I've looked through thousands, including officers whose court martial is mentioned in the CSR. The most that usually appears in the CSR is the verdict of the court, though sometimes the specifications and charges are set forth along with the defendant's response. It is my understanding that the Confederate court martial records in Richmond were lost/destroyed at the end of the war, along with many other Confederate records. I am told that court martial records for a few units survive.