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  • San Francisco 49ers Jed York, left, receives the NFC Championship...

    San Francisco 49ers Jed York, left, receives the NFC Championship trophy after the team defeated the Green Bay Packers 37-20 at Levi's Stadium on Sunday, Jan. 19, 2020. (Randy Vazquez / Bay Area News Group)

  • San Francisco 49ers head coach Kyle Shanahan, right, receives a...

    San Francisco 49ers head coach Kyle Shanahan, right, receives a hug from his father Mike Shanahan after winning the NFC Championship game versus the Green Bay Packers at Levi's Stadium on Sunday, Jan. 19, 2020. (Randy Vazquez / Bay Area News Group)

  • San Francisco 49ers' George Kittle (85) celebrates with San Francisco...

    San Francisco 49ers' George Kittle (85) celebrates with San Francisco 49ers' quarterback Jimmy Garoppolo (10) after winning the NFC Championship game at Levi's Stadium in Santa Clara, Calif., on Sunday, Jan. 19, 2020. The San Francisco 49ers defeated the Green Bay Packers 37-20. (Jose Carlos Fajardo/Bay Area News Group)

  • San Francisco 49ers general manager John Lynch raises their NFC...

    San Francisco 49ers general manager John Lynch raises their NFC Championship trophy after defeating the Green Bay Packers 37-20 at Levi's Stadium in Santa Clara, Calif., on Sunday, Jan. 19, 2020. (Ray Chavez/Bay Area News Group)

  • San Francisco 49ers' Raheem Mostert (31) celebrates after winning the...

    Randy Vazquez / Bay Area News Group)

    San Francisco 49ers' Raheem Mostert (31) celebrates after winning the NFC Championship game versus the Green Bay Packers 37-20 at Levi's Stadium on Sunday, Jan. 19, 2020. Mostert would score four touchdowns in the game. Randy Vazquez / Bay Area News Group)

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Cam Inman, 49ers beat and NFL reporter, San Jose Mercury News, for his Wordpress profile. (Michael Malone/Bay Area News Group)
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SANTA CLARA – Jed York wouldn’t gloat about his Super Bowl-bound 49ers inside a triumphant locker room Sunday night.

He took a deep breath. He measured his words, balancing a prideful tone with that of a boss seeking more.

“I’m proud of these guys for how hard they worked,” York told me in an exclusive interview. “They have to stay focused this week and then get into the craziness of Miami the week after.”

The 49ers’ CEO won’t say it so I will: The state of this franchise has never been better in the 20 years under York-family control.

Dr. John York quietly agreed with my assessment when I ran it by him last week, after he sauntered out to admire practice, even with his left foot in an orthopedic boot because of a problematic ligament.

“Pretty special,” the elder York said of this season.

This was a few days before the 49ers clinched a Super Bowl LIV berth and the NFC Championship. They did so by virtue of Sunday’s 37-20 win over the Green Bay Packers – at Levi’s Stadium, the 6-year-old venue that the Yorks and so many others diligently worked to build for legendary moments like this.

Left tackle Joe Staley agreed this is the best the 49ers’ organization has looked in his 13 seasons. “From the top to the bottom, I’ve felt very close with everybody, and everybody is on the same page,” Staley said. “It’s just a fun place to come to work every day.”

A rebuilt roster is blossoming with stars. Kyle Shanahan and his coaching staff remain devilishly cunning. Count in general manager John Lynch and the front-office hierarchy, not to mention the 49ers’ business operations, and “things are running pretty smooth right now,” said a long-time agent, wishing to remain anonymous.

Kyle Shanahan hugs Joe Staley after winning the NFC Championship Game over the Green Bay Packers. (Randy Vazquez / Bay Area News Group) 

When confetti shot through the South Bay’s misty air Sunday night, the 49ers had won a Super Bowl berth on their home turf for the first time since January 1995 at Candlestick Park.

“It was cool having the stage out there and sharing it with my family. But one more game,” Staley said. “Being able to have another opportunity in Year 13 is special.”

Their 2012 team won its NFC title in Atlanta, and losing to Baltimore in the ensuing Super Bowl serves as a haunting reminder this special season still needs a happier ending.

Said Jed York: “We’ll celebrate tonight, and it goes back to what Bill Walsh said, ‘We’re champions today but we have one more to go.’ ”

Shanahan and Lynch are harmoniously leading the way, which they signed up to do in 2017 with six-year contracts meant to stabilize a freefalling franchise.

It’s not too early to talk contract extensions. Right, Jed?

“I want those guys here for a long time,” York responded. “If they want to do something, I’d be happy to do it.”

This season’s 15 wins are no fluke. While they won only 10 games combined in the previous two seasons, it’s the abundant losses, especially close ones, that melded this team for adverse times (see: December 2019 gauntlet).

Kyle Shanahan looks up at the stands after winning the NFC Championship Game. (Randy Vazquez / Bay Area News Group) 

“Those guys do have each other’s back,” York said. “Not that it’s been perfect. Not that we’ve made every single right decision.

“But when the culture is right, when you have each other’s back, it gives you a chance. You need some level of talent, which we have on this team, but if you don’t have the culture, you have no chance.”

Shanahan turned 40 last month; York hits 39 in March. They get each other. And Shanahan was especially appreciative of Sunday night’s surprise: He received the NFC’s George Halas Trophy from his father, Mike, the 49ers’ offensive coordinator on their last Super Bowl winner 25 years ago.

“To get a trophy handed by anyone is really cool, but especially Jed making my dad an honorary captain,” Kyle Shanahan said. “Jed told me it was special for his mom when his uncle handed her the trophy before they won. And Jed planned all that and did that.

“It was pretty cool, I didn’t know what was going on, but it was pretty cool that it happened there at the end. It was pretty special.”

John Lynch congratulates Jimmy Garoppolo after winning the NFC Championship Game. (Jose Carlos Fajardo/Bay Area News Group) 

Indeed, when the 2012 team won the Halas Trophy in Atlanta, former owner Eddie DeBartolo made a surprise appearance and awarded it to his sister, Denise DeBartolo York, Jed’s mother.

Two years later, the 49ers imploded, Jim Harbaugh split for the University of Michigan, and then neither Jim Tomsula nor Chip Kelly stuck around past a season.

York stuck around, even when media critics called for his ouster.

“I own this football team. You don’t dismiss owners,” York said Jan. 2, 2017 after dismissing Kelly and general manager Trent Baalke. “I’m sorry that that’s the facts and that’s the case, but that’s the facts. I’m going to do everything I can to get this right.”

He didn’t know how long this recovery would take. He knew it wouldn’t be a quick fix. Shanahan emphasized that, too, upon landing such a long-term deal for a first-time head coach, and one for his hand-picked, first-time general manager.

Staley said he was “pretty close to retiring” before Shanahan, upon arrival, convinced him otherwise. “Sitting down with Kyle and seeing his vision for this franchise, it was huge for me to ride it out and see it through,” Staley said.

Despite the 0-9 start in 2017 and then a 4-12 death march after Jimmy Garoppolo’s Week 3 knee injury, the Yorks publicly and privately expressed faith in Shanahan and York, so much so that it was foolish to think this was a Super Bowl-or-bust season.

Super Bowl, it is.

As Shanahan choreographed Sunday’s rout, upstairs in a suite were Lynch and his vice presidents of player personnel Adam Peters and Martin Mayhew, who were caught on camera celebrating together after Raheem Mostert’s fourth touchdown run.

“I didn’t want them to ever feel the third year was the ‘hot seat’ year, because we had not done well up to that point,” York said. “You had a run before with Jim and Trent, and some really good football teams, and we needed to make sure they knew, the players knew, the fans knew that there was no hot seat for those guys.

“They have a runway and I believe in them to rebuild this culture, and they did.”

Kyle Shanahan celebrates with his family after winning their NFC Championship Game. (Aric Crabb/Bay Area News Group) 

The term “culture” gets thrown around every time a team makes a coaching do-over, and the Yorks sure have sought regaining a championship culture over their ownership tenure. See: Steve Mariucci, Dennis Erickson, Mike Nolan, Mike Singletary, Harbaugh, Tomsula, Kelly and, at last, Shanahan.

This team has developed a tight-knit bond from all their wins and losses over the years, both on and off the field. That includes the York family’s tragic loss of Jed’s younger brother, Tony, who died by suicide on Dec. 7, 2018.

Two days later, an emotional Jed York received the ceremonial game ball after the 49ers beat the Denver Broncos. He responded with this tear-jerking, locker-room address:

“This team is going to be a champion,” Jed York vowed on Dec. 9, 2018. “I’m going to leave a ring when we get one for my brother, and I want everybody to look around this room and know how good we can be.

“Believe in this brotherhood. Believe in this guy, believe in this guy, believe in yourselves. And it’s going to be about mental toughness, it’s going to be about what we can get through more than the other 31 teams out there, and we are going to do it. You guys keep fighting your asses off and I’m going to give my brother a ring.”

Fast forward to Sunday night. York tried slipping unnoticed through the locker room. He’s intentionally left this season’s spotlight up to his coach, his general manager, his trophy-hunting players.

Upon acquiescing to an interview, amid congratulations from locker-room guests, York made sure to temper the celebration, seven years after missing out on the Lombardi Trophy.

“We’ve gone through it, but the Chiefs are such a good football team,” York said. “I mean, Andy (Reid) is a Hall of Fame coach. You’ve got a young, future Hall of Fame quarterback (Patrick Mahomes).

“It’s going to be a battle. It’s going to be the toughest game we’ve played all year, and we’ve played a lot of tough ones.”