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Early offensive struggles and injuries present the 49ers with their biggest challenge yet

It’s just Week 4, but I think this is the biggest uphill battle that Kyle Shanahan has faced so far in his career.

Seattle Seahawks v San Francisco 49ers Photo by Thearon W. Henderson/Getty Images

At two different points mid-way through the season, the 49ers were two games under .500, with the postseason looking like a distant dream. Somehow, someway, Kyle Shanahan managed to lead them to a 7-2 record down the stretch to backdoor their way into the playoffs. Then proceeded to follow it up with two road playoff wins, bringing his career postseason win total to four.

The 49ers were at a crossroads last season, as they sat at 3-5 with the Rams coming into Levi’s Stadium for a Monday Night prime-time showdown. This season, the 49ers sit at 1-2, with the Rams strutting into Santa Clara for another Monday Night contest.

However, I think the challenge this season is going to be far greater for Kyle Shanahan than it was last season.

Let’s start with his coaching staff. Shanahan doesn’t have his trusted right-hand man Mike McDaniel to help design his run game anymore. Tight ends coach Jon Embree and quarterbacks coach Rich Scangarello are no longer in town. Running backs coach Bobby Turner is away from the team this season.

That’s a lot of coaching talent that the 49ers let walk out the door. They’ve replaced those coaches with some popular names in the NFL circles, but they don’t have the same continuity as an offensive staff that they’ve had in years past.

Beyond that, the 49ers spent the entire offseason crafting and designing an offense that would take advantage of 22-year-old Trey Lance’s skillset—using more vertical patterns in the pass game and designing a rushing attack that would heavily lean on Lance’s ability to run. Then, one and a half weeks into the season, the 49ers lost Lance for the year and have had to punt that portion of their playbook into the sun.

Now, there’s certainly an advantage with Jimmy Garoppolo being the one under center and a ton of familiarity between Garoppolo and Shanahan’s system. But I think that also comes at a disadvantage in raising this offense's ceiling.

Garoppolo’s skillset best utilizes the middle of the field between 0 and 20 yards. That being said, defenses have now had five years' worth of film on Garoppolo, and it’s becoming harder and harder for Shanahan to not use all parts of the field on offense.

With the offense struggling and ranking in the bottom 10 of most statistical categories, Shanahan’s going to have to dig deep and find creative ways to unleash this passing attack.

Health-wise, Shanahan won’t be without their best offensive player (pound for pound) in Trent Williams for at least the next 4-6 weeks. That’s a major blow to an offensive line that relied heavily on the veteran expertise of the best tackle in the sport. Shanahan’s already trying to work back George Kittle and Garoppolo into game shape multiple weeks into the season, and he’ll be doing it without Williams or his top running back in, Elijah Mitchell, for the next eight weeks.

On top of this, the 49ers are already in the hole at 1-2, dropping two games where the defense played stellar, and the game was there for the taking.

Beyond the injuries, the early offensive struggles, and coaching staff turnover, I think Kyle Shanahan’s biggest challenge is going to mend his relationship and trust with Jimmy Garoppolo.

The head coach-quarterback relationship is the most important in the NFL, and the 49ers’ duo of Shanahan and Garoppolo clearly seems to be off-kilter. They may have a somewhat healthy working relationship, but in order for the 49ers to maximize their roster and talent this season, those two men have to come together and lead this team.

Shanahan was able to climb out of a similar hole last year and come out like a King (even though they lost in the NFC Championship game, I thought they were playing with house money).

Can he do it one more time?