How Kyle Shanahan, John Lynch make 49ers CEO Jed York's job easier

SANTA CLARA -- Thirty-two NFL teams, 16 in each conference, compete for a spot in the Super Bowl each season.

Using that math, the 49ers are doing a lot better than most when it comes to advancing to play for the honor of raising the Lombardi Trophy.

After all, it was back in January of 2013 when the 49ers defeated the Atlanta Falcons in the NFC Championship Game to send the organization to its sixth Super Bowl appearance.

The 49ers are back. The club departs the Bay Area on Sunday en route to Miami, where they will play the Kansas City Chiefs in Super Bowl LIV on Feb. 2.

“Being in the Super Bowl seven years ago, it doesn’t seem that long,” 49ers CEO Jed York said. “Except for the deep valley we went into between.”

The 49ers didn't have a winning record in the five seasons prior to 2019.

This vintage of the 49ers is a more cohesive group than the last group to make it this far. There was never harmony at the top of the organization with coach Jim Harbaugh and general manager Trent Baalke – two men who clearly did not enjoy each other’s company.

Harbaugh accurately described himself as “moody and complicated.” Baalke never seemed comfortable in his role as general manager, seemingly a better fit for traveling solo in rental cars through the middle of the country on scouting trips.

The dysfunction between coach and general manager did not reflect well on York, the man ultimately responsible for the pairing of the top two football minds in the organization.

Things are much different now.

When York was asked how the combination of coach Kyle Shanahan and general manager John Lynch has made his life easier, he answered, “How much time do you have?”

York, 39, no longer has to be concerned with any petty personality conflicts at the highest levels of the football side.

“Neither one is trying to elbow the other to get to the front of the line to say, ‘I’m the executive of the year,’ ‘I’m the coach of the year,’” York said. “They’re happy for the other one. They’re happy for everybody’s success.”

The tenure of Harbaugh brought instant success, along with instant conflict and tension. The daily turmoil and uneasiness were small prices to pay for three consecutive trips to the NFC Championship Game, along with a Super Bowl appearance.

But the foundation of the organization began to give way and the structure began to tip after a while.

During the 2014 season, with the 49ers en route to an 8-8 finish, it became an irreparable situation. Within moments after Harbaugh stepped off the podium following the 49ers’ season-ending victory, the organization issued a press release to announce a “mutual parting.”

But things got a whole lot worse before they got better. York and Baalke swung and missed with the one-and-done hirings of Jim Tomsula and Chip Kelly.

Finally, York determined a complete overhaul was warranted. Baalke, who engineered the previous coaching hires and let the roster fall into a state of disrepair, was out as general manager.

Amid calls for York to take a step back – including a banner being flown from a plane above Levi’s Stadium – he actually assigned himself more responsibility. He and executive Paraag Marathe led the search for a new head coach.

York was looking for an offensive-minded head coach who could groom and develop a quarterback. He wanted a coach and GM combination that could work well together, get along and pull in the same direction during adversity.

Shanahan immediately told York that the 49ers’ roster was horrible. York said he knew within 10 minutes that their visions were aligned.

They convinced Shanahan to leave his position as Atlanta Falcons offensive coordinator to lead the organization. Shanahan brought Lynch out of the FOX TV booth to join him as general manager.

Ultimately, York offered the coach and GM six-year contracts because of the massive rebuild that was required and to send a message to the players, fans and media. There would be no talk of anyone being on the hot seat through the expected lean years. York said he viewed the contracts as two years to clean up the mess, followed by the first year of four-year contracts.

This season, was Year 1, according to York.

“The knocks you heard on Kyle when you did your reference checks was, he thinks he knows everything,” York said. “You had those negative things. But he’s just honest and direct. And it’s hard when you’re in my position to know when somebody is really being truly honest and direct and when somebody’s kissing your ass. And Kyle is very, very direct.”

York said he does not believe his management style has changed much in the 10 years he has been in his position as CEO. But what makes his job easier now is the honest, direct communication he shares with Shanahan and Lynch.

“I’m trying to do things the right way,” York said. “But just because I want to do it doesn’t mean it’s the right way to do it. And it’s great to have somebody, ‘Nah, we need this.’ ‘This is what’s going to be the problem, and this is how we’re going to try to fix it.’ And that’s what I have with Kyle. It’s awesome to go to work every day.”

Although Shanahan had never been a head coach, his coaching smarts were never in question. Shanahan just wanted his best opportunity to succeed with ownership that shared his commitment to win – at any cost.

“You want to go to a team that truly the most important thing is to win a Super Bowl,” Shanahan said. “Everyone says that, but your actions show it. I got to really believe in Jed by spending about four hours with him in that first interview.

“Everything that he said, he backed up, and you never know until you get somewhere. But, since I've been here for three years now, whether we started 0-9 or went 4-12 our second year, that's only gotten stronger, and he's validated that more and more each day.”

Shanahan found the right man with whom to work. Shanahan and Lynch might not agree on every decision, but there has never been any hint at problems with the two men.

In fact, Lynch does not generally travel during the season to scout college prospects because Shanahan values the support and company he gives him when he remains at the team’s facility in Santa Clara.

Those atop the organization are sharing in the successes of this season after sharing in the miseries of the previous two years. Lynch was selected as NFL Executive of the Year by the Pro Football Writers of America, an honor from which Shanahan and York can take satisfaction, too.

Lynch has rewarded Shanahan’s hunch and gamble.

After a long, distinguished playing career, Lynch has grown into the position as the team’s top personnel executive. The 49ers have not hit on every draft pick or every free-agent acquisition. But there is little to critique about the direction the club has taken under his stewardship.

“He makes every team he’s a part of better,” York said of Lynch. “He makes every team he’s part of a championship-caliber group.”

[RELATED: Cutting Reuben Foster defines Shanahan-Lynch era]

York’s tenure in charge with the 49ers has been a lot more difficult to define.

He has been encouraged to fire himself. He let it be known he was never going to go away. He has remained confident in his own ability to put the pieces into place to, eventually, accomplish the only goal he has publicly stated: Win a Super Bowl.

York and Lynch, in a lot of ways, are powerless at this point. The 49ers’ 53-man roster is set. Shanahan and his players have everything they need to go win one more game.

York does not have a big presence in the locker room, though tight end George Kittle said the players know they can count on him if they ever need something.

“One thing I love about him, he doesn't force his presence on us,” Kittle said. “He says, ‘Hey, I'm here for you guys if you ever need me. I'm supporting you. I'm your guys' biggest fan. If you ever need anything, I'm always here to help.’ "

"But he never forces things on guys. I love that about him, and I have the utmost respect for him and how he handles this organization.”