Kelly wants gig, but 49ers have company in Payton race

Chip Kelly covets the job and has alerted the 49ers. Sean Payton is interested, too, but when Tom Coughlin and the Giants parted ways Monday, New York likely became Payton’s most desired destination if he leaves New Orleans. Mike Shanahan also is casting his sights on Santa Clara, but he’s in Miami today, interviewing with the Dolphins.

Seems the Niners’ coaching search is as cluttered right now as their messy, 5-11 season.

CEO Jed York and general manager Trent Baalke are thinking big for their next hire, but the question is whether they can back up their ambitions with a major name — as many doubt. Other than saying the next coach would come from the outside, they offered few clues Monday.

“We’re in need of somebody who can win Super Bowls,” was about all York said in a rare media address at Levi’s Stadium, a day after coach Jim Tomsula was fired after one season.

In that case, Payton, Shanahan and Mike Holmgren fit the requirement. Shanahan has two Super Bowl trophies on his resume, while Holmgren and Payton have one each. Among them, Payton is the only one who has been an NFL coach of late, another reason he’ll be the first big domino to fall in the coaching derby. It’s also why the Saints coach is believed to be at or near the top of the Niners’ wish list.

Payton met with Saints general manager Mickey Loomis to discuss his future Monday. Indications are the sides are willing to part ways under the right terms. Payton is the kind of big name that can wake up the 49ers’ sleepy fan base and improve their tarnished brand, but how badly do York and Co. want him? He would command a high price in terms of power and authority, leaving doubts that he could co-exist with Baalke and York in the long term. Both have been relutant to relinquish control in the past, though Baalke and Payton are fellow disciples of the influential Bill Parcells.

Baalke insisted that control over personnel matters was “way overblown.”

“For this to work, both individuals have to be in sync, working together for the same goal and purpose,” he said. “It doesn’t matter who has the ultimate final say. What matters is that you make the decision together, and when the decision is made, you move forward and don’t look back.”

The Saints also would want a draft choice in return for Payton, who is still under contract, probably a pick in the second round. In the Niners’ case, that would be 39th overall, a price they might consider too steep given their overall shortage of talent.

The 49ers also would have stiff competition for Payton in the Giants, who offer stable ownership in the Mara family, a proven quarterback in Eli Manning, a star receiver in Odell Beckham Jr. and the No. 1 market, a package that is said to have Payton’s attention.

What the Niners don’t have are a large talent base or a proven quarterback. What they do have: The seventh pick in the draft and the fifth-most money to spend in free agency this offseason.

“We have work to do,” Baalke conceded. “There’s no question about that. The good thing is, we have the ammunition. We’re sitting in a very good situation relative to the [salary] cap and cash. We’ve got 12 draft picks or around that number. We have the ability to do something that we didn’t have going into this one.”

Baalke has been given the responsibility to choose the next coach. As with all significant matters in the organization, York will retain veto power.

“Trent’s role is to find the next head coach and continue to build this roster and get us back to championship form,’’ York said.

Baalke assembled a team whose overall talent level ranks in the bottom-third in the league. For that reason, critics say he isn’t qualified to pick the next coach.

Whether the new coach would inherit Colin Kaepernick remained in doubt after the quarterback added a damaged right thumb to his list of health problems. In December, he underwent surgery to repair a torn labrum in his left shoulder. Last week, an MRI exam confirmed that Kaepernick had a torn ligament in his right (throwing) hand. He said the injury occurred in a loss against the Seattle Seahawks on Oct. 22. He was scheduled to seek a second opinion on surgery in Vail (Colo.) this week.

If Kaepernick is on the roster on April 1, $11.9 million of his contract will be guaranteed.

“For me, that’s not a date I’m concerned with,’’ Kaepernick said Monday. “I feel like I’m going to be playing football regardless of April 1, April 2. I’m doing everything I can to be healthy as soon as I can. Once again, I’m preparing to be healthy and win the Super Bowl. That’s all my focus is.”

The 63-year-old Shanahan has 20 years of head coach experience. His offenses are known for their balance between the run and pass. He’s well-schooled in quarterback play — Hall of Famer John Elway had his best seasons under him. He also drafted Kirk Cousins, who has come into his own this season.

Shanahan last coached three years ago, in Washington, and his Redskins tenure didn’t turn out well. Some believe that he ran rookie sensation Robert Griffin III into the ground, a rough ride from which the quarterback has yet to recover. And did Elway make him or did he make Elway or was it some of both?

The 49ers could turn to someone such as Kelly or Cincinnati Bengals offensive coordinator Hue Jackson.

If anyone knows offense, it’s Kelly. He has delivered point-scoring success at the college and pro levels, especially when he had a quarterback that fit his system. He also has a positive relationship with Niners personnel director Tom Gamble, with whom he worked in Philadelphia.

Sooner or later, would Kelly want considerable input in personnel matters? He is not a skilled communicator, a weakness that led to distant relationships with many Eagles players. It’s doubtful his offense could thrive with Kaepernick or Blaine Gabbert at the controls.

The 50-year-old Jackson has a straight-forward approach that plays well in the locker room. Under his watch, quarterback Andy Dalton was having his best season before an injury. A finalist for the Cal job four years ago, the one-time Pacific quarterback and coach is no stranger to the Bay Area, having gone 8-8 with the Raiders in 2011 before he was dismissed after one season.

The competition for top coaches eased a bit when Indianapolis, in a shocker, agreed to a four-year extension with Chuck Pagano, while San Diego retained Mike McCoy.

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