49ers facing a summer of questions

This is my Monday column on the top-five questions the 49ers face this summer.

Even though the 49ers are among the odds-on favorites to win the Super Bowl, like any other team, they confront certain issues.

Two of their best players – Justin Smith and Frank Gore – are in their 30s and declining. The 49ers’ offensive MVP last season – Michael Crabtree – tore his Achilles tendon in OTAs. He could sit out the whole season. The 49ers’ schedule is brutal. Their division is the best in the NFL, and their three division rivals – the Seahawks, Rams and Cardinals – improved this offseason.

Five make-or-break questions face the 49ers right now. Here they are:

1. Is Justin Smith vulnerable? He was indestructible from 2002 to 2011, when he didn’t miss a single game. In 2011, he was the best defensive player in the NFL, almost single-handedly willing the 49ers to the Super Bowl.

Before he tore a tendon in his elbow in New England last season, the 49ers’ defense gave up a league-best 14.15 points per game. After his injury, the 49ers gave up a league-worst 29.67 points per game, including the playoffs. In the Super Bowl, Justin Smith was the worst 49ers defender on the field, according to Pro Football Focus. The Ravens’ rookie left guard, Kelechi Osemele, manhandled Smith all game.

Smith is the 49ers’ most important player this season. He’s 34 and coming off the first major injury of his career. Is he vulnerable to tearing the ligament again?

If Smith can bounce back to his pre-injury form, the 49ers’ defense might be able to lead the team back to the Super Bowl. But if Smith continues his decline, the 49ers will be forced to win games with their offense.

2. Will Colin Kaepernick have a sophomore slump? Many teams didn’t know what to expect when they faced Kaepernick last season (for example, the Bears and the Packers). This season, teams will be prepared for him. They’ve spent the whole offseason figuring out a way to defend him and the read option. How will Kaepernick adjust to the defenses’ adjustments?

In the Super Bowl, the Ravens hit Kaepernick every time he handed the ball to a running back on a read-option play. There’s a good chance other defenses will adopt that strategy this season. How will Kaepernick respond to the licks? Will the 49ers use a more traditional offense this season to protect him? Will he have to operate more often as a drop-back passer who has to go through his reads and find the open receiver? Can he excel playing that style for a full season?

He also has areas of his game he needs to clean up. Call it game management, the stuff Alex Smith was good at. Kaepernick needs to improve his pre-snap reads – identifying the defense and choosing the correct plat at the line of scrimmage. He also needs to call the plays quicker. The 49ers had to burn far too many timeouts to prevent delay-of-game penalties. And Kaepernick needs to stop fumbling snaps when he’s lined up under center. He fumbled nine times last regular season.

To make things even tougher for Kaepernick, he’ll be without four of his main receivers to start the season. Delanie Walker signed with the Titans. Randy Moss is gone. Mario Manningham probably will miss training camp and start the season on the Physically Unable to Perform List as he rehabs a torn ACL and PCL. And you already know about Crabtree’s Achilles. That leaves Kaepernick with a bunch of unproven youngsters, plus Anquan Boldin and Vernon Davis.

Kaepernick has to develop chemistry with all of these receivers, including Davis. Those two did not develop a strong on-field connection last season. Kaepernick never even looked his way during the 49ers’ final-five offensive plays in the Super Bowl.

3. How strong is the running back corps? The 49ers’ have the best run-blocking offensive line in the NFL, but how good are the running backs? Frank Gore was very good last season, but he’s slowing down. He averaged 5.1 yards per carry between the tackles, but just 3.8 yards per carry outside the tackles. And he has worn down the past two regular seasons, failing to register a 100-yard rushing game in the regular season after Week 8 in 2011 and 2012. The 49ers have to keep him fresh for the playoffs, so he can’t carry the load in the regular season. He needs help.

Kendall Hunter helped carry the load last season. He was the only 49ers running back who could run inside and outside effectively. He averaged 5.2 yards per carry and was one of the best change-of-pace backs in the NFL. He even looked like he could eventually become a featured-back before he tore his Achilles in New Orleans Week 12. Now, he’s starting training camp on the PUP list.

He’s a small running back who relies on quickness and explosion. Hunter may not regain 100 percent of his explosion until the second half of this season or next season.

The 49ers’ other change-of-pace running back is LaMichael James. Last season, he was not an effective inside runner, but he’s gained 10 pounds since then. If he can give the offense what Hunter gave them last season, the 49ers should once again have an elite running game. If James cannot establish himself as an inside threat, the 49ers’ running game could be predictable – Gore up the middle and James around the outside.

4. Who will emerge as a deep threat? The 49ers currently have just one – Vernon Davis. They need one more. Last season they typically had at least two on the field at a time with Davis, Walker, Manningham and Moss. Those deep threats made opposing safeties play deeper, which helped the 49ers’ running game. The deep threats also complemented Kaepernick’s rocket arm and aggressive style. He threw the ball 20 or more yards downfield 30 percent of the time last season, more than any other quarterback.

Besides Davis, who is Kaepernick going to throw to downfield this season?

Probably not Anquan Boldin. He’s a possession receiver.

Last year’s first round pick, A.J. Jenkins, is fast, but was not a deep threat at the University of Illinois. He was a possession receiver.

The 49ers’ fourth-round pick this offseason, Quinton Patton, was a deep threat at Louisiana Tech, but he may not be fast enough to run past NFL cornerbacks.

Kyle Williams is on the PUP list. He’s injury prone and unproven.

The best candidate to become the 49ers’ second deep threat may not be a wide receiver at all. He may be a rookie tight end. Vance McDonald, a second-round pick, could be deep threat No.2 like Delanie Walker last season.

McDonald isn’t as fast as Walker, but he’s big and fast for his size and can outrun some safeties. Jim Harbaugh and Greg Roman like to use tight ends as deep threats. At Stanford they used Coby Fleener, a tight end, as their primary deep threat.

If McDonald or someone else does not emerge as a deep threat, opposing defenses will play closer to the line of scrimmage to try to take away the 49ers’ strength, their running game.

5. Can Greg Roman improve his play-calling? Roman’s offense averaged 6.0 yards per play last season, third-best in the NFL. But he faces a tougher task this season. Without Crabtree, Roman will have to proactively get the ball to Vernon Davis in the passing game. Roman primarily used Davis as a decoy to get other receivers open the past two seasons. This season, Davis has to be a consistent weapon, not a mere decoy. Roman should script at least one pass to Davis in the first 10 to 15 plays of every game. That’s what Bill Walsh would do.

If the 49ers can solve each of these five issues, they should return to the Super Bowl. If they cannot find the solutions, they could miss the playoffs altogether.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for the Press Democrat’s website. You can reach him at grantcohn@gmail.com.

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