49ers notes: Coaches are in flux; what does Garoppolo’s injury means for a trade?

This is shaping up to be Kyle Shanahan’s toughest offseason since becoming 49ers head coach.

Consider: Shanahan has been forced to overhaul his entire offensive coaching staff, which comes at the same time the team is making a switch at quarterback from veteran Jimmy Garoppolo to youngster Trey Lance (presumably — more on that in a bit).

Gone is offensive coordinator and top lieutenant Mike McDaniel, who was hired to become the head coach of the Miami Dolphins. McDaniel was a sounding board and game planner who had been with Shanahan since both were offensive coaches with the Houston Texans in 2006.

Joining McDaniel in Miami is receivers coach Wes Welker and tight ends coach Jon Embree, who were instrumental in developing stars like Deebo Samuel and George Kittle.

Running backs coach Bobby Turner, a legend in coaching circles, is expected to take a year away from working, John Lynch told reporters at the scouting combine in Indianapolis this week. That means it could be more difficult for the 49ers to find and develop running backs found either late in the draft or in undrafted free agency, which has been a calling card since Turner joined Shanahan on the staff in 2017.

Previously unheralded names like Raheem Mostert, Matt Breida, Jeff Wilson and Elijah Mitchell have all been key contributors that were heavily influenced by Turner, who worked with Mike Shanahan and the Denver Broncos back in the 1990s. Turner leaves big shoes to fill both as a coach and evaluator of lesser-known talent.

Former quarterbacks coach Rich Scangarello recently bolted to become the offensive coordinator for the University of Kentucky, meaning Lance will have a no position coach to learn from.

49ers coaching moves

Given all the vacancies that need filling, it’s not surprising Shanahan elected to skip the combine altogether this week, instead staying home to assemble his staff while handling draft meetings virtually. Lynch told reporters he believes the hires filling the open positions will be made official in the coming weeks.

“Kyle and I talked and we felt like his time and his staff’s time were best spent there (back home),” Lynch said Wednesday. “The great thing about what we’ve learned over the last couple years is when we’re interviewing players, those respective coaches and coordinators and Kyle will get on the zooms. And so even though they aren’t here, they are here and we talk every night and we talk every morning, so communication is good. We just felt like that was best for our organization this week. And they’re having a real productive week, getting that scheme work done, getting used to each other as a staff and also taking part in the evaluation process.”

The 49ers have become a desirable organization for up-and-coming coaches. They’ve had two coaches move on to become head coaches in the last two hiring cycles (Robert Saleh to the Jets in 2021 and McDaniel to the Dolphins), and there’s a good chance current defensive coordinator DeMeco Ryans will be a candidate again next winter after interviewing for the Vikings’ opening in January.

In some ways hiring new coaches could be a positive. It could lead to new blood, new energy and new philosophies inside the building to provide fresh perspectives. And with Lance likely to take over at quarterback, the new coaches could help implement a new scheme that’s different from what the team ran with Garoppolo.

Lance, who is more athletic and has a much bigger arm, shouldn’t be confined to making short throws the same way Garoppolo was. In those ways the 49ers could be significantly different next season, which falls in line with Shanahan’s track record for being schematically adaptable and, in some ways, a trail blazer.

Shanahan’s coaching tree has continued to grow all over the league. A slew of his former assistants are now head coaches, including Sean McVay, the recent Super Bowl winner, Matt LaFleur and McDaniel, with offshoot coaches from similar systems getting head jobs in recent years in Cleveland (Kevin Stefanski), Cincinnati (Zac Taylor) and Denver (Nathanial Hackett).

Which means as more and more teams run Shanahan’s version of the West Coast offense heavily predicated on outside zone running schemes and play action, the more pertinent it is for Shanahan to adapt to the next cutting edge, which is where Lance comes in.

Lance, who turns 22 in May, has posted on Instagram from Los Angeles this week, where it’s likely he’s begun his offseason work with specialized quarterback coaches. Lance wouldn’t say in his exit interviews who exactly he would be working with, but there’s a reasonable chance he’ll reunite with John Beck, whom Shanahan sent Lance to leading up to the draft last year before he was taken third overall.

What Garoppolo’s shoulder surgery means for his trade market

News dropped this week of Garoppolo needing surgery to repair a capsule in his throwing shoulder that was first reported by ESPN.

What does it mean for his trade market?

Probably not a whole lot. Teams already knew Garoppolo had injury concerns. He’s missed 25 starts since 2016 because of shoulder, knee, ankle, calf and thumb injuries. He sustained the recent shoulder injury in the wild card-round win over the Dallas Cowboys while trying to protect his throwing thumb he injured Week 16.

“It was one of those injuries where the recommendation from multiple doctors was let’s try rehab first and see if the pain and some of the other symptoms go away,” Lynch said. “And that was the hope obviously, but that wasn’t the case as time went on. And I think in the last couple days, he had another visit where the decision was made to go ahead and have that surgery. Anytime you have surgery, it’s not a minor deal. Anytime it’s the throwing shoulder, I understand the significance, but it is described as a minor surgery and Jimmy is going to be fine.”

But the surgery could change the timing of a trade. After all, teams interested will likely want to see Garoppolo’s medical file and imaging of the shoulder after the procedure before making a deal. He’s not expected to resume throwing until June or July, which means he won’t be able to throw during the entire offseason program with his new team. With March 16, the official start of the 2022 league year, just around the corner, the timing does the 49ers no favors.

The key for San Francisco is getting Garoppolo’s $25.5 million off the books as soon as possible. The surgery could delay that, which means the team could have a little less financial clarity when free agency begins. The 49ers, as of this writing, are roughly $4.5 million over the salary cap. They could use the cap space from a Garoppolo trade to retain free agents like guard Laken Tomlinson and/or defensive tackle D.J. Jones, or add a veteran cornerback.

Can the 49ers release Garoppolo?

But Garoppolo has a $7.5 million guarantee for injury, which means releasing him would create some $18 million in cap space rather than the full $25.5 million. That guarantee is offset, meaning it would go away if and when Garoppolo signs for at least that much with another team. Releasing Garoppolo could be an option if the team decides getting out from his cap hit is the top priority rather than waiting for teams to suss out Garoppolo’s medical file and make trade offers.

If the 49ers release Garoppolo, he’ll still carry a $7.5 million cap hit that will likely disappear when he lands elsewhere, but it could impact the team’s ability to spend in free agency when it kicks off March 16, when the team has to be under the salary cap with its top-51 salaried players.

Of course, NFL teams have a way of manipulating contracts and salaries to make the numbers fit. The team is expected to restructure contracts from their expensive stars to create room. Kittle, Arik Armstead and perhaps an extension for safety Jimmie Ward could create some $24 million in cap space. That, on top of moving Garoppolo, either through trade or release, could give the 49ers ample cap space to be aggressive with outside free agents or retaining their own.

What Garoppolo’s surgery does is potentially muck up the timing and potentially lessen the value he has on the open market, especially if teams know the 49ers are desperate to get rid of cap hit and could end up releasing him anyway.

The silver lining for San Francisco is that even coming off surgery, Garoppolo could be the best available quarterback this offseason. That’s because the signs are pointing to Aaron Rodgers staying with the Packers, Russell Wilson not being made available in a trade with the Seahawks and Deshaun Watson being unwilling to settle the 22 civil lawsuits against him for sexual misconduct and inappropriate acts.

The draft class is also considered weak at quarterback, leaving teams like the Steelers, Commanders, Panthers, Colts, Buccaneers and Broncos in the Garoppolo market.

“A lot of people need or want quarterbacks right now and he’s obviously a guy they’d look at,” Lynch said. “So, yes, we have listened, but he’s a part of us and he’s going to work diligently to get back from this surgery. It’s just preliminary, I haven’t even talked to Jimmy yet. But it sounds like that’s the decision right now to go ahead and have that. And you guys know the same thing I know, which is that he can return to throwing late June, early July and the prognosis is really good. So that’s all good stuff.”