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What the San Francisco 49ers Must Do in the Second Half of the NFL Season

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COMMENTARY | The first half of the 2013 NFL season wasn't without trials and tribulations for the defending NFC champions. The San Francisco 49ers had to deal with injuries to their top-two wide receivers from a season ago in the form of Michael Crabtree and Mario Manningham, both of whom haven't taken a single snap thus far this season.

Linebacker Aldon Smith missed the final five games before San Francisco's bye after being arrested for a DUI and checking himself into rehab following the 49ers Week 3 blowout loss at the hands of the Indianapolis Colts.

Head coach Jim Harbaugh, who is now 30-9-1 with the 49ers, was dealt his first two-game losing streak. San Francisco fell to the Seattle Seahawks and Indianapolis by a combined 56-10 score. It was also the first time the 49ers were under .500 since Harbaugh took over as head coach in 2011. Meanwhile, the Seahawks seemed destined to run away with the NFC West. Young quarterback Colin Kaepernick also had his first real struggles of his short career, compiling zero touchdowns and four interceptions in those two games.

Needless to say, the 49ers needed to get their ship in order. What proceeded was a dominating five-game winning streak that saw the defending conference champs defeat their opponents by a combined score of 174-61. Fresh off their bye, let's take a look at what the 49ers need to do in order to maintain that high level of play and put themselves in a position to repeat as conference champions.

Get the Passing Game on Track

It's purely a subjective term without any real context when indicating that the 49ers boast NFL's 32nd-ranked passing offense. While true, they have also attempted the least amount of passes in the league. Looking at it through a mathematical lens, this means that the 49ers possess an average passing offense at this point in this season.

This shouldn't come as much of a surprise considering that they were without both Crabtree and Manningham in the first half of the season. Once those two weapons return at near full health, the 49ers should be more consistent through the air.

With that said, there are other reasons why San Francisco hasn't had much more than an average passing game up to this point. Inconsistency in terms of accuracy and comfort level in the pocket seemed to plague Kaepernick through the first four games of the season. While receivers didn't help the young quarterback, he struggled progressing past his initial read. It was also Kaepernick's lack of comfort level with receivers not named Anquan Boldin that impacted his consistency through the air. It remains to be seen whether this will change in the second half of the season, but if the last four games are any indication then Kaepernick seems to be on the right track. Getting Manningham and Crabtree back surely won't hurt either.

Let Kaepernick Play His Game

It seemed as if Kaepernick struggled letting the game naturally flow to him through the first six games of the season. Pure conjecture on my part, but San Francisco's unwillingness to let him run the ball led to a lot of these struggles. The only time Kaepernick really gained yards on the ground during those first five games were through compromise on his part. In short, there really weren't a lot of designed run plays. This changed in the final two games leading up to San Francisco's Week 9 bye. It's not a coincidence that Kaepernick put up 122 yards and three touchdowns on 18 rush attempts while tallying a 103.8 quarterback rating during that span.

In order for the 49ers to take full advantage of Kaepernick's rare skillset, it is going to have to let him play his game. This means throwing out the conservative nature of going away from the read option in order to protect their most valuable asset. Simply put, he's less valuable when you don't let him play his game. It does, however, appear that the 49ers coaching staff started to understand this in the final two games of the first half.

Ease the "Newcomers" Back Into the Lineup

While it might be difficult for fans to understand, the 49ers need to make sure that the players they have returning from injury and rehab (Aldon Smith) aren't thrown to the wolves out of the gate. The next two games against winning teams might be important, but so is the remainder of the schedule and the stretch run into December. The idea here is to make sure they are 100 percent and ready to go as the season draws to a conclusion and the playoffs begin.

For some, this may be hard to do. A prime example of that is going to be Mario Manningham, who immediately becomes San Francisco's No. 2 wide receiver behind Anquan Boldin with Michael Crabtree still sidelined. We will acquire a good understanding of where San Francisco's coaching staff stands on this come Sunday against the Carolina Panthers. If Kyle Williams is inactive and LaMichael James is called on to return kicks, it will become readily apparent that the 49ers are planning to push Manningham right out of the gate.

Aldon Smith, who is also slated to play, will likely be mixed into the outside linebacker rotation with Ahmad Brooks, Dan Skuta and rookie Corey Lemonier. That seems to make the most sense, especially with Lemonier playing so well in his stead. This will enable Smith to get his sea legs back and ready to go full time when San Francisco takes on the New Orleans Saints in Week 11.

As it relates to Cornellius Carradine and Eric Wright, their playing time will largely depend on what they show in practice. Neither is an anointed starter and will be playing more of a reserve role moving forward this season. The larger question here is what San Francisco plans on doing with Crabtree, who is coming off a serious Achilles injury. He's also the most valuable player returning to the 53-man roster. Again, it should all be about easing him into a full-time role.

Continued Domination

San Francisco has blown away four of its last five opponents and is playing some darn good football. It does need to make sure that this domination continues and other aspects of the game progress nicely. It's the idea that the 49ers can afford to improve in specific areas while still maintaining a high level of play in other areas.

I touched on the passing game before, but will now focus on the defensive side of the ball. While the 49ers have held offenses in check over the past five games, they haven't necessarily done a great job getting to the quarterback. This is evidenced by the fact that Jacksonville Jaguars quarterback Chad Henne was not sacked a single time in Week 9. That has to be discouraging considering San Francisco was going up against two backup offensive tackles. Of course the addition of Aldon Smith to the lineup is going to help, but Vic Fangio's defense needs to find other ways to get pressure on the quarterback. If they are able to do this, the 49ers are going to be incredibly difficult to beat.

End Game

At the end of the day, most experts had San Francisco at 6-2 or somewhere near that level entering its Week 9 bye. We shouldn't be too surprised that this squad is among the best teams in the conference. With that said, there are a lot of areas of improvement. Some of these areas will get better simply by the additions of talented players off injury and other off-field situations. Other areas were likely worked on during the bye week. It's now all about putting everything together, beginning against the Panthers on Sunday.

Vincent Frank has been covering the National Football League for three years. He started out writing for Bleacher Report and is currently the head editor at eDraft and a columnist at Pro Football Focus. Vincent co-hosts a weekly radio show called "Football Debate Central" with former NFL player Ryan Riddle and has seen his work featured on CNN, BR and Los Angeles Times, among many other outlets.

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