Kyle Shanahan, right, used to work with his father, Mike, left, who coached 49ers GM John Lynch . (Keith Allison/Flickr)

Kyle Shanahan, right, used to work with his father, Mike, left, who coached 49ers GM John Lynch . (Keith Allison/Flickr)

49ers meet with presumptive picks for head coach, GM openings

The 49ers’ two most vital positions — head coach and general manager — have gone unfilled for 26 days since CEO Jed York cleared house.

All indications suggest the team knows who it wants for the next era, but York has maintained that he wants the selections to prove they work well together. And with Kyle Shanahan’s current employer, the Atlanta Falcons, set to play in the Super Bowl next Sunday, the decision to hire him and George Paton, the team’s presumptive pick for GM, has been put on hold.

“We need to make sure that the head coach and the general manager know each other, have a good understanding for each other,” York said on Jan. 2 in Santa Clara. “Doesn’t mean that they had to have worked together in the past, but they have to have a good respect for each other and a good understanding and know that they have similar visions and philosophies on building a football team.”

The Niners met with Shanahan and Paton in Atlanta on Friday for their second official interview. They also spoke with Terry McDonough, an executive for the Arizona Cardinals, on Saturday, the team’s Vice President of Communications confirmed on Twitter.

At this point, the 49ers have little leverage over Shanahan after all other candidates were either ruled out or withdrew from consideration over the last few weeks. That led Mike Florio of Pro Football Talk to speculate about the offensive guru to offer a position to his father, Mike.

“Ultimately, the question will be whether the 49ers are willing to risk losing Kyle,” Florio wrote. “Before they cross that bridge, they need to be confident that a viable Plan B (or, as the case may be, Plan D) is available.”

All roads lead to Shanahan and Paton taking over operations in the South Bay, and a lot can happen in a week before the 49ers are allowed to officially hire their choice to be their four head coach in four years. But Shanahan revealed to Peter King, of MMQB, earlier this week that the team’s turmoil in recent years wasn’t a disqualifying factor for him.

“I’ve believed it for a while: You always want the right opportunity,” he said. “I’ve been battle-tested. I think I went through a lot of situations that a lot of coordinators in the league haven’t. I think I’ve had to handle some situations or got some attention, mostly negative, that usually head coaches only have to deal with. So I think that’s helped me prepare from that standpoint.”george patonkyle shanahanNFLSan Francisco 49ersterry mcdonough

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