Since he was benched in November and subsequently went on injured reserve with an injury to his non-throwing shoulder, quarterback Colin Kaepernick and the 49ers appeared to be in line for a mutual parting.

But even as Kaepernick is beginning rehabilitation of shoulder, thumb and knee surgeries, the early stages of the 49ers’ search for a new coach look to be lining up favorably for a possible Kaepernick return in 2016.

At least two of the top candidates for the 49ers’ vacant head-coaching job are known to have coveted quarterback Colin Kaepernick in the past. Chip Kelly interviewed for the opening on Thursday, and Hue Jackson is scheduled to interview on Sunday.

Kelly, whom the Philadelphia Eagles fired on Dec. 30, reportedly attempted to acquire Kaepernick from the 49ers in the offseason. Kelly’s up-tempo offenses at Oregon functioned best with a mobile quarterback. Kaepernick’s unique skillset could to be a nice match for Kelly’s system.

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In 2013, two years after his one-and-done tenure as Raiders coach, Jackson told Peter King of the MMQB how much he and Al Davis wanted Kaepernick in the draft. The 49ers moved up to No. 36 to select Kaepernick. The Raiders almost certainly would have taken Kaepernick at No. 48.

 

"I think about it all the time, believe me,'' Jackson said. "No question in my mind we wanted it to happen, and no question I thought it could happen. We wanted the kid in the worst way.''

Kaepernick told King, “Coach Jackson told me before the draft they were going to do everything they could to try to get me.”

Kelly and Jackson are two of the top candidates to replace Jim Tomsula, who was fired after going 5-11 in his only season.

The 49ers interviewed Buffalo assistant head coach/running backs Anthony Lynn on Thursday. The team is scheduled to interview Cleveland offensive coordinator John DeFilippo on Friday. The 49ers have also requested an interview with Tampa Bay offensive coordinator Dirk Koetter but no meeting has been scheduled.

A source indicated the 49ers have not ruled out Adam Gase or Mike Shanahan, two candidates from last year’s search. A year ago, Gase and Shanahan both expressed excitement over the possibility of working with Kaepernick, the source said.

Every candidate the 49ers are known to have contacted about the job opening has experience on the offensive side of the ball. The next head coach will likely get to choose whether the team retains Kaepernick or attempts to part with his scheduled $14.3 million pay for next season.

The day after the final game of the season, Kaepernick said his focus is on getting healthy for as much as the team’s offseason program as possible. With a new coach, the 49ers are allowed to begin workouts on April 4.

"I'm under contract. I'm a 49er," Kaepernick said. "I'm doing everything I can to make sure I'm prepared for next season."

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Kaepernick’s $11.9 million base salary is guaranteed for injury only. It becomes fully guaranteed if he remains on the roster on April 1.

“I’m not worried about April 1 to be honest with you,” 49ers general manager Trent Baalke said. “I’m more worried about getting him healthy and getting him ready for the offseason program. So, whatever that date is that the medical staff steps up and says, ‘Look, he’s ready to go.’ That’s when he’ll go.”

Blaine Gabbert, who started the final eight games of the season, also remains under contract to the 49ers for next season.

Kaepernick was benched before his physical ailments were revealed. He completed 59 of his passes with six touchdowns and five interceptions in eight games. His passer rating was a career-low 78.5, as the 49ers were 2-6 in the games he started.