[thrash]

Military prisoners are not service members for the duration of their sentence -- they are prisoners. They don't have rank, receive no pay or benefits, and (inter alia) don't wear any military insignia. Any sentence served is in addition to their contracted enlistment. If the offense is serious enough to warrant incarceration at Fort Leavenworth it probably includes a dishonorable discharge, however, effective immediately upon release.

CID is the Criminal Investigation Division -- think detectives. Once they present their evidence at trial, they are out of the picture. There is an entire MOS within the Military Police trained for prison work, as well as POW and displaced civilian operations in wartime. They would be the ones transporting any military prisoners.

It is almost certainly logistically simpler for the Disciplinary Barracks to arrange a secure interview room in their own facility and have DHS (or whoever) come to visit the prisoner there, than to transport him somewhere else. (Of course, if the investigation requires the fixed Alien Mind Reading Squids facility in Area 51, that would change things.)

The psych wards in military hospitals are not set up for long term care. As far as I know, a patient declared permanently incompetent would receive a psych discharge and be turned over to whatever mental hospital is handy. Someone who poses a national security risk -- given what he knew before he cracked -- might be sent to St. Elizabeth's for special safekeeping.

Murder and manslaughter are punishable "as a court martial may direct," up to and including death or life in prison for premeditated murder or murder in commission of some other major crime (rape, etc.). If premeditation can't be proved, the prosecutor will probably try for a manslaughter conviction.