49ers' Jed York still confident in GM John Lynch, coach Kyle Shanahan

John Lynch and Kyle Shanahan have 10 wins in two seasons with the 49ers, but Jed York's plan all along has been for long-term stability. AP Photo/Marcio Jose Sanchez

PHOENIX -- The San Francisco 49ers endured many key injuries in 2018, and they narrowly avoided another.

Moments after learning that quarterback Jimmy Garoppolo had torn an ACL in Week 3 against the Kansas City Chiefs, CEO Jed York found the nearest wall in an Arrowhead Stadium suite and threw his hardest punch.

"I thought I broke my wrist when I heard that he tore his ACL," York said. "Unfortunately, it was a stud. You've got to find the drywall, that's the key. It looks so much better to put a hole through the wall as opposed to finding a stud and potentially break your wrist."

In some ways, that anecdote ideally sums up the Niners' 2018 season. A year that began with the promise of breaking through the metaphorical wall of their recent struggles ended with a resounding thud.

What remained was a 4-12 season in which the 49ers did not take the step forward they'd hoped. Without Garoppolo for a full season, they were left with more questions than answers.

As coach Kyle Shanahan and general manager John Lynch head toward the halfway point of the six-year deals they signed in 2017, progress is more difficult to see than it was when the Niners closed the 2017 season with a Garoppolo-fueled five-game winning streak.

York said at this week's NFL annual meetings that he is as confident in his handpicked coach and general manager tandem as ever and didn't sound like someone who is growing impatient that results have yet to come.

"I think that was a big thing knowing that we had instability, knowing that we had multiple coaches in multiple years and going through that, we wanted to send a message to everybody that Kyle and John, to our existing players, to our fan base, to potential future free agents, these guys are going to be here for a long period of time," York said. "Knowing that they're both first time in their job, we need to make sure that we get through some of that trial and error. There are going to be things that get broken, there are going to be mistakes that are made, but how do we learn from that and how do we get better?

"There were a lot of things that you don't know what you don't know when you're in those positions, and I think it's been interesting to watch these guys really come together and show they are a stronger bond today than what they were two years ago, and it's only getting stronger."

After sweeping out former coach Chip Kelly and general manager Trent Baalke following a two-win 2016 season, York prioritized cohesion and stability. Both had been lacking in the organization since just before the departure of Jim Harbaugh. So, York wanted to find a coach and general manager he knew could work well in tandem, honestly talk through problems and still be in alignment when it came time to make big decisions.

Shanahan and Lynch had an easy rapport from the time they were hired, having known each other long before their union with the Niners had become official. Still, a friendship and a business partnership are different things, and with both coach and GM in their jobs for the first time, there figured to be some growing pains.

It helped that they began their working relationship during the more relaxed offseason, not during the season when Shanahan is "a little more uptight."

"So they start to learn my personality when I'm easier to deal with and when I'm not," Shanahan said. "I see it with them, too, and you start to understand what stressed each other out, what things each other likes. It just like any human relationship. You start to learn each other, and I think you get better at working with each other the more you know."

While the Niners' leadership is working in lockstep, the reality remains that winning reigns supreme -- and with 10 wins in two seasons, there hasn't been nearly enough.

"[York's] support has been constant and so that's not news to us," Lynch said. "But the reality is everybody knows that you better have results. This is probably the most results-oriented business that I know. We understand -- we expect that out of ourselves, which is most important."

York appreciates the way Shanahan and Lynch have gone about rebuilding the roster and is a believer that the team is acquiring both good football players and strong locker room personalities. That has yet to translate to the desired wins, but York recalled the time it took for Scot McCloughan and Baalke to build the team that went to three NFC Championship Games from 2011 to 2013. That team didn't become a winner overnight, but the seeds for it could be seen in the makings of a stout defense in 2009-2010.

This Niners team doesn't have those defensive pieces, but York sees potential in Garoppolo, who he believes can be "very special," combined with promising young players such as defensive tackle DeForest Buckner and tight end George Kittle.

They key now for York & Co. is to ensure that the only studs they find are ones who can help lead the Niners to more victories.

"We want to make sure we have the right core groups of people on our team," York said, "and build this thing where we can compete for a consistent period of time, and hopefully it's a Patriot-type deal where you've got 10, 15, 20 years of sustained success. That's my aspiration to have a team that can do that."