Specifics about service should be determined from documents in this officer's military file. It's usually possible to determine the senior officer in command at a given time by checking signatures on requisitions for clothing and equipment which appear in service files.
I'm assuming that you already have copies of this file, although the National Archives doesn't always copy the documents mentioned. Copies made by message board resources always include requisitions, pay receipts &c.
After Pemberton's appointment, an announcement of staff officers and their positions (medical director, chief quartermaster, adjutant general &c.) would have been made. It should be in the O.R.