No. 1 on his agenda is determining who, if anyone, from Mike Singletary's regime will stay on as a coach next season.
Monday Harbaugh met with the team's current stable of assistant coaches and one coach who looks like he won't be back is defensive coordinator Greg Manusky.
Harbaugh granted the team's top defensive play caller for the past four years permission to speak with other teams. Arizona and Dallas are both reported to be interested in Manusky.
He could also return to San Diego, where Manusky was an assistant coach before joining the 49ers, if current Chargers Defensive Coordinator Ron Rivera becomes the head coach in Carolina.
Harbaugh is expected to name current Stanford Defensive Coordinator Vic Fangio as the 49ers top defensive coach but there could be competition for him as well.