49ers’ worries go well beyond QB

The 49ers lead the NFL in missed tackles, are one of two teams with zero interceptions and their entire wide receiver corps has 16 fewer receptions and 100 fewer yards than the Saints’ Michael Thomas. There’s more.

Only three teams have allowed more sacks, they might have problems with poise and their top edge rusher doesn’t have a sack entering Sunday’s road game against the Chargers.

The point of this is to pose a question: Even if quarterback C.J. Beathard is the second coming of Jimmy Garoppolo, are the rest of the 49ers good enough for them to go anywhere in 2018?

In the aftermath of Garoppolo’s torn ACL, there has been much discussion about Beathard’s ability to save the season that’s started 1-2. However, the focus on their most important position has obscured the mounting evidence that, even with a franchise QB with a healthy left knee, their rebuilding project had some serious foundational cracks. When asked on Friday about the areas that could stand improvement, head coach Kyle Shanahan’s answer highlighted the all-encompassing issues.

“If we could get off the field on third down on defense, and we could stay on the field on offense on third down,” Shanahan said, “I think that would change a lot of things dramatically.”

Perhaps this shouldn’t be too surprising, given Shanahan and general manager John Lynch inherited a 2-14 team 19 months ago. The new regime has overhauled the roster — only 11 players from the 2016 team remain — and have emphasized youth during the process.

In a 38-27 Week 3 loss to the Chiefs, six of the 11 defensive starters had made fewer than 15 career starts. On Thursday, cornerback Richard Sherman, 30, pointed to a lack of poise as a reason Kansas City opened the game with touchdown drives of 57, 84, 75, 72 and 68 yards.

“Our coaches have done a great job of game-planning and putting us in position,” Sherman said. “It’s just going out there and taking it to the game field. I think sometimes the bright lights get to some people. And we need to get back to being more detailed and being able to say: ‘Hey, we’ve seen this in practice. We treated like this in practice. This is how we need to react in the game.’ ”

The 49ers’ decision-makers have made it clear where some of the remaining holes exist on the roster. Before the regular season, they aggressively pursued a trade for All-Pro edge rusher Khalil Mack, who would have replaced Cassius Marsh (zero sacks).

After the season opener, they looked into a trade for oft-suspended and ultra-talented wide receiver Josh Gordon. The 49ers’ wide receivers have just 22 catches for 298 yards and three touchdowns this season, although Marquise Goodwin’s quadriceps injury has contributed to those paltry numbers.

However, the 49ers also have sprung leaks in surprising areas.

Last year, Garoppolo’s quick release was cited as a reason the 49ers allowed just eight sacks in his five starts after surrendering 35 in their first 11 games. However, they had allowed 13 sacks this season before Garoppolo exited late in the fourth quarter last week.

“Our pass protection has got to come along,” left tackle Joe Staley said. “There’s leaks that are there. It’s the tale of two different (lines). It’s either perfect or there’s leakage somewhere and a guy gets home. We have to make our mistakes be unnoticeable mistakes instead of now a lot of those mistakes are obvious. We’ve just got to shore up our protections.”

Their pass-protection issues could be magnified with Beathard starting. In 2017, his willingness to hang in the pocket won him hard-earned respect, but it also explained why he took 17 sacks and 52 hits in his five starts.

In Beathard’s second season, Staley expects the 2017 thirdround pick will be improved.

“I think last year it was kind of just play football and figure it out as you go,” Staley said. “I think he’s got a stronger understanding of the offense than he had last year when he was just kind of thrown in there. … I think that bodes well for us with C.J.”

Given his added experience, it wouldn’t be a surprise if Beathard is better.

But even if he channels Garoppolo, the 49ers’ season is unlikely to be saved unless they get better in several other areas.

Eric Branch is a San Francisco Chronicle staff writer. Email: ebranch@sfchronicle.com Twitter: @Eric_Branch

D. Ross Cameron / Special to The Chronicle Quarterback C.J. Beathard is expected to be improved in his second season as a 49er.