A person familiar with the club's thinking indicated as much Tuesday, noting that Manuel and general manager Omar Minaya still are discussing the composition of the staff.
No indication was given about Ken Oberkfell, who became the first-base coach in June when Manuel replaced Willie Randolph and Randolph's first base coach, Tom Nieto, was dismissed. But it is likely Oberkfell, highly regarded by the club, would remain with the organization, returning to his previous assignment as Triple-A manager, if he were not retained on the big league staff.
Guy Conti, who served as the bullpen coach, almost certainly will be retained in some capacity. The fate of Luis Aguayo, Manuel's third-base coach and a Minor League field coordinator before the managerial change, was unclear as was that of Alomar's son, Sandy Jr., who served as catching instructor last season.
None of the staff members had contracts for beyond the 2008 season.
Warthen was recognized for eliciting a degree of consistency from erratic Oliver Perez after he replaced Rick Peterson, who had been dismissed with Randolph and Nieto. He had begun the season, his first back with the Mets organization after two years with the Dodgers, as pitching coach for the Triple-A New Orleans Zephyrs.
The Mets' pitchers appreciated his simple and direct approach, a contrast to Peterson's more pedantic manner.
Johnson completed a full season as hitting coach for the first time. He had been appointed to the position at the All-Star break in 2007, replacing Randolph's choice, Rick Downs. He had been the first-base coach in the first half of the 2007 season and a hitting coach in the Mets' Minor League system for the preceding four seasons.
Johnson came under some public fire for the Mets' uneven run production, particularly when the team faded late in the season. But a number of players, notably Ryan Church and later Brian Schneider, benefited from his guidance. And the shortfall of the other, higher-profile hitters -- Carlos Beltran and Jose Reyes -- was not attributed to the former switch-hitter.
Alomar Sr. moved to the Mets in 2005, Randolph's first season. He was the bench coach in 2005, the first-base coach in 2006 and the third-base coach in 2007 and last season until the managerial change. What role he would fill in 2009 has not been specified.
The identities of men outside the organization favored by Manuel are not clear. Manuel's staff in six seasons managing the White Sox was relatively stable. Three of the coaches in his first season -- Nardi Contreras, Wallace Johnson and Joe Nossek -- worked for five seasons, and Von Joshua worked for four.
Marty Noble is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.