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Colin Kaepernick was the 49ers' leading rusher against the Cardinals.
Colin Kaepernick was the 49ers' leading rusher against the Cardinals.USA TODAY Sports

5 Adjustments the San Francisco 49ers Must Make in Week 4

Dan MoriSep 24, 2014

The San Francisco 49ers are 1-2, and although they started 2013 with the same record, things feel a lot different this season.

They are searching for their identity and also struggling with injuries and off-field problems. Aldon Smith is suspended for the first nine games of the season, and it remains to be seen whether anything will happen to Ray McDonald.

The 49ers now play the Philadelphia Eagles, who are 3-0 and second in the league in total points scored. If the 49ers do not right the ship immediately, they could fall to 1-3 and put their season in jeopardy very early on.

Let's take a look at some adjustments the 49ers must make in order to give themselves the best chance to defeat the Eagles.

No. 5: Get Aaron Lynch into the Game More Frequently

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Aaron Lynch has the ability to rush the passer.
Aaron Lynch has the ability to rush the passer.

With Aldon Smith out for the first nine games of the season, Dan Skuta and Corey Lemonier are trying to fill in. Last year, Skuta and Lemonier did a credible job when Smith missed six games as he underwent treatment for substance abuse.

Skuta plays in the 49ers' base defense and has been solid. Lemonier typically enters the game on passing downs but has not made an impact.

In three games, Lemonier has no sacks and only four tackles. To make matters worse, he is having trouble getting any pressure on the quarterback, which is his primary job.

Over the spring and summer, Lemonier put on weight in an attempt to gain strength. However, that has not worked and may have cost him some of his explosive outside speed.

The 49ers have not been able to generate consistent pressure on the quarterback when they rush only four men. This lack of pressure was an issue in the 49ers' loss to the Bears in Week 2. The 49ers defensive secondary has not played well and is a work in progress.

Defensive coordinator Vic Fangio called a lot more blitzes against the Cardinals. He deserves credit for trying to generate more pressure and protect his very suspect secondary.

Unfortunately, when the 49ers were unable to get to Arizona quarterback Drew Stanton, he found open receivers and made the defense pay.

The 49ers were playing without starting cornerback Tramaine Brock, but Parrish Cox did a credible job. The other defensive backs were beaten or looked lost, as breakdowns in communication also factored in. 

With Lemonier largely a non-factor in the 49ers' first three games, it's time to give Aaron Lynch more playing time. Lynch is a dynamic pass-rusher and has shown an ability to be a disruptive force—something the 49ers defense desperately needs at this point.

No. 4: Make Some Changes on the Offensive Line

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Joe Looney started in place of Alex Boone against the Cowboys.
Joe Looney started in place of Alex Boone against the Cowboys.

The 49ers offensive line is not the dominant force it has been in years past. Joe Staley, Mike Iupati and Daniel Kilgore have done a decent job, but the problems on the right side of the line have been magnified.

Right tackle Anthony Davis missed the entire preseason and has not played in the 49ers' first three games. He is dealing with a hamstring injury, and it does not look like he will be playing anytime soon.

When Davis is ultimately able to get back into the lineup, he will likely be rusty and not in top condition. 

Alex Boone's holdout cost him the entire preseason, and he has struggled at times. He has missed several blocks and looks rusty.

In the fourth quarter against Arizona, safety Tony Jefferson blitzed right up the middle, and Boone totally whiffed on him. The result was a sack and a hard hit to the legs of Colin Kaepernick. It was fortunate that the 49ers quarterback was not injured.

Jonathan Martin has been equally unstable at the right tackle position. His clipping penalty, which was not necessary because the play was already past the defender, cost the 49ers dearly. Martin has also had trouble in pass protection.

One possible solution is to reinsert Joe Looney back into the right guard spot and move Boone outside to tackle, at least until Davis is ready to play.

A move this bold is unlikely, but it should be considered. The lack of continuity and weak performance of the 49ers offensive line are alarming.

No. 3: Be More Stubborn with the Running Game

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Frank Gore's expression is worth a thousand words.
Frank Gore's expression is worth a thousand words.

The San Francisco 49ers abandoned the running game against the Arizona Cardinals, and the result was another loss. 

The 49ers utilized multiple wide receiver sets, and that confused the Cardinals early in the game. However, the Cardinals adjusted, and after the 49ers scored touchdowns on their first two drives, they were unable to score again.

The most glaring omission of the 49ers offense was the complete disappearance of the running game. Frank Gore had six carries for 10 yards, and Carlos Hyde had three carries for 13 yards. For Gore and Hyde to get only nine carries is a mistake in planning and play-calling.

Quarterback Colin Kaepernick led the team with 13 carries for 54 yards. Many of the successful runs he had came on read-option plays in the first half. He faked to the running back and kept the ball himself. This worked early, but the Arizona defense adjusted and took this away as the game progressed.

The 49ers' offensive philosophy seems to be in a state of flux. In recent years the offense has featured a staunch ground game, and the San Francisco offensive line is ideally suited to run blocking.

This year, we are seeing a lot more multiple wide receiver sets and a greater focus on the passing attack. With a healthy Michael Crabtree, Anquan Boldin and Stevie Johnson, plus the addition of Brandon Lloyd and Bruce Ellington, the 49ers have leaned on a more wide-open approach.

The 49ers must be more balanced between run and pass. Abandoning the ground game means that Gore and Hyde are far less effective. They are both excellent power runners, and if the 49ers are more stubborn with the run, they can wear down the opposing defense.

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No. 2: Better Offensive Adjustments Throughout the Game

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San Francisco offensive coordinator Greg Roman has not made proper adjustments during the game.
San Francisco offensive coordinator Greg Roman has not made proper adjustments during the game.

The San Francisco 49ers have started games very well. The offensive game plans have been very productive, and the 49ers have outscored their opponents by a 59-16 margin in the first half of games. For this, Jim Harbaugh and Greg Roman are to be commended.

However, opposing defenses have adjusted after the 49ers' early success and have shut down the San Francisco offense. The 49ers have scored a total of only three points in the second half of all their games. They are being outscored 52-3 in the second half.

This means Roman and the offensive coaches are not making good adjustments to counter what the opposing defense is doing. Play-calling has been questionable, and there is no excuse for scoring only three points in six quarters of football.

Defensive coordinator Vic Fangio is working with a depleted cast of players, but there is no reason for the 49ers' offensive futility over the second half of these games. Roman is simply being out-coached.

No. 1: Eliminate the Penalties

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Has Jim Harbaugh lost control of the 49ers?
Has Jim Harbaugh lost control of the 49ers?

Penalties have hurt the 49ers and were a major reason for the last two losses. Even in their win against Dallas to open the season, they committed 11 penalties for 78 yards.

The trend has gotten worse. Against the Chicago Bears, the 49ers committed an astronomical 16 penalties for 118 yards. The situation should have been addressed and rectified immediately.

However, the flags continued to fly in Arizona. The 49ers were penalized at the most inopportune times, keeping Arizona drives alive or killing their own. Nine penalties were enforced for 107 yards, and another three penalties were not accepted.

On one of the flags, Arizona was called for holding and would have been pushed back. Instead, after an incomplete pass, Chris Culliver jumped into the face of the Cardinals receiver with his idiotic trash talking. He was called for the penalty, which offset the Arizona flag and meant the down was simply replayed.

The Cardinals got the first down and were able to hold onto the ball. Had Culliver just shut up, it would have been 1st-and-20. The 49ers could have held in a three-and-out and gotten the ball back immediately.

Anquan Boldin also was flagged for a critical penalty when the 49ers had driven the ball to the Arizona 6-yard line. He got into a jawing match with the Cardinals defender and gave him a head butt. The result was 15 yards, which quickly turned into 30 when Jonathan Martin was called for clipping on the very next play.

This snuffed the 49ers' drive, which could have resulted in the go-ahead touchdown. Instead, the 49ers had to attempt a long field goal, which was blocked.

Boldin was extremely critical of the officials following the game. As reported by Taylor Price of 49ers.com, Boldin insisted that defenders were taking shots at him the whole game. He did acknowledge his mistake with the head butt, however.

The officials are also calling illegal contact on pass plays, even with incidental contact beyond the five-yard allowable zone. The 49er defensive backs have not adjusted to that and are called on this all too frequently.

Then, even when they make good defensive plays, the officials in their overprotective mode are flagging the 49ers. It happened to Patrick Willis twice and also to Dan Skuta. Forty-five yards in personal-foul penalties on hits that should not have been called.

This is a purely editorial comment, but it seems as though, perhaps subconsciously, the very negative press the 49ers have received recently with the off-field incidents involving Aldon Smith, Chris Culliver and Ray McDonald has caused the officials to be more apt to call penalties on the 49ers.

Granted, some of the calls involve their own lack of discipline, like Boldin and Culliver, but it seems borderline calls are also going against the team.

Former 49ers great Brent Jones was recently interviewed on KNBR radio, the 49ers' flagship station. His comments were a stinging criticism of the way the current group of players are conducting themselves. Jones was incensed by the lack of discipline the team is displaying.

"As a team, we need to be smarter," he said. "Ego and selfishness is above team." 

Jones went on to say that when Bill Walsh and George Seifert were coaching the team during his time with the 49ers, "the team always came first over individuals."

It seems as if many players in this current group of 49ers have lost this concept.

Who is to blame for all of the penalties? The players, coaches or management? 

In reality, they are all to blame. The current culture of the 49ers has gotten away from execution, precision and class and drifted into intimidation and a lack of personal and institutional control. The lack of accountability is an organizational issue.

Undoubtedly, the 49ers coaches are imploring the players to be smarter and play with greater discipline. However, we have not seen that on the field. One must wonder if the players are all still listening to Harbaugh and his staff. 

Tim Kawakami of the San Jose Mercury News reported on Harbaugh's comments following the loss. Harbaugh acknowledged that the team must play better and smarter but said very little beyond that. 

The 49ers are very fragile at this point, and with a tough Eagles team coming to town, they could easily be 1-3 after this Sunday. If that happens, we may start to see more evidence that Harbaugh and his staff have lost this team.

Stats courtesy of NFL.com.

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