In 2005, Schaefer received the Distinguished Alumni Award from UConn, primarily for his achievements on that College World Series team.

On May 31, 2005, Buddy Bell took the reins as permanent manager and Schaefer returned to the bench coach position.

He also managed the New York Mets' Class AAA team in Tidewater to an International League championship in 1985.

Schaefer then moved on to the Boston Red Sox organization, serving as a special assignment scout and later the director of player development from 1994 to the midseason of 1998.

Although Schaefer received positive notices for his work as the Red Sox' player development chief, he clashed with general manager Dan Duquette and was fired during the summer of 1998; several minor league managers and coaches, including Geren, departed the organization with Schaefer, who spent the next three years as a special assistant to the general manager of the Baltimore Orioles before returning to the Royals in 2001 as a bench coach and infielders coach.