The National Archives has transcripts of the courts martial proceedings on microfilm.
Lt. Cmdr. Augustus P. Cooke, GCM (General Court Martial) 3288, and Daniel P. Upton, GCM 3289, both on Microfilm Roll 110, Vol. 101, General Courts-Martial Transcripts, Record Group 125.
I would bet that the folks here at History-Sites (banner ad at top of page) could get a copy for you quicker than you can get it straight from National Archives. Don't think that's on their list of items they handle, but it wouldn't hurt to ask.