John,
I can't answer all of your questions, but I do know from my own family research that ADAH has some lists that includes men not found in their on-line database. My gggrandfather and his twin brother, both of whom served in the 26th/50th Alabama, are found on a hand-written list at ADAH compiled by a member of their company 40 or 50 years after the war. Their service is confirmed by records from NARA, but their names are not in the ADAH on-line database.