By Dan Durkin-

(CBS) In a league full of rules to protect the quarterback and limit down-field contact, teams are incentivized to throw the ball, which fills the Sunday sky with flying pigskins. Thus, the 49ers formula for winning – playing lights out defense and running the football – could be considered passé. However, the 2011 49ers were a muffed punt away from representing the NFC in the Super Bowl, so clearly, there’s still room at the top for teams who play “old school” football.

It becomes even more impressive when you consider that 2011 was head coach Jim Harbaugh’s inaugural season, one in which he didn’t have the benefit of a full off-season to properly install his system due to the lockout.

Prior to Harbaugh’s arrival, the 49ers were mired in an eight year tailspin. Guys like Dennis Erickson, Mike Nolan, and Mike Singletary took turns failing, compiling a 46-82 mark as the 49ers stumbled into NFL irrelevancy. Despite the shortened off-season, the talented 49ers bought into Harbaugh’s philosophy and they’re back to prominence.

General manager Trent Baalke also deserves credit for the 49ers quick turnaround. Baalke joined the 49ers in 2008 as an area scout, and in very short order worked his way up through the ranks. The 49ers are one of the deepest teams in the league, and Baalke’s moves – particularly on special teams and defense – have reshaped the roster, enabling their physical brand of football.

Even after making a concerted effort to improve the talent at wide receiver – signing Super Bowl hero Mario Manningham, future Hall-of-Famer Randy Moss, and using a first-round pick on A.J. Jenkins (Illinois) – the 49ers remain a power running team. This is out of necessity given limitations in pass blocking and at the quarterback position, manned by 2005’s top-overall pick, Alex Smith.

Smith – whose status is still uncertain due to a concussion – has benefited from Harbaugh’s arrival. Over the past season and a half, he’s cut down on interception totals while increasing his quarterback rating. This means he is operating the offense as designed: make quick decisions with the football, if your secondary/tertiary read isn’t open, either tuck it and run, or throw the ball away. Basically saying: punting is fine.

Surely, the 49ers were hoping for more than just a game manager when they drafted Smith, but that has proven to be his apex. What makes Smith’s low ceiling even more difficult to deal with is that just 23 picks later a guy named Aaron Rodgers was selected by the Green Bay Packers.

Knowing how special their defense is, Baalke and Harbaugh flirted with Peyton Manning. All offseason I wrote this match made too much sense to not happen. Think about the 49ers right now with Manning. Scary.

If Smith is unable to go on Monday night, Colin Kaepernick would start at quarterback. Kaepernick is a very gifted runner, adept at the zone-read option, and poses an entirely different challenge for a defense. However, eventually you have to stretch a defense vertically to get the extra safety out of the box, something Kaepernick hasn’t proven to be capable of.

Former 2009 first-round draft pick wide receiver Michael Crabtree has emerged as the 49ers top receiving threat. He’s on pace to post career highs in yards, receptions, and touchdowns, but his production relative to other No. 1 receivers is pedestrian.

Tight end Vernon Davis is one of the league’s most gifted athletes and is a matchup nightmare for safeties or linebackers, yet somehow the 49ers have not been able to get him properly involved in their game plans. Of Davis’s 29 receptions, 20 have gone for first downs, and nine have gone for more than 20 yards. For a team that runs the ball as effectively as the 49ers do, they should scheme more play-action shots to Davis up the seam of the defense.

The bread and butter of the 49ers offense is their running game. Through ten weeks, the 49ers are one of four teams to have more rushing attempts than passing attempts (Seattle, Houston, and Washington are the other three), and they lead the league with a 170-yard per game average.

Frank Gore is on pace to put up his highest rushing total since 2006, and his 5.4 yards per carry matches his career high, good enough for the second highest mark in the league for running backs with 100+ carries. Gore is a shifty in-between the tackles runner who doesn’t possess blazing speed, but has a nose for the first-down marker and goal-line. Gore is just three rushing touchdowns shy of the 49ers franchise record (50).

The 49ers break several “rules” with their running game, frequently splitting both Gore and second year player Kendall Hunter in the backfield at the same time in a pro set. Hunter is a great compliment to Gore, showing exceptional quickness and burst through tight running lanes. Since Hunter’s arrival, the 49ers are 18-1-1 in games where he and Gore combine for 20 or more carries.

While the 49ers offensive line has deficiencies with pass protection, they’re a dominant run blocking group. Offensive coordinator Greg Roman has installed the most diverse running scheme in the NFL and is very creative with pulls and trap plays. Their pulling lineman get to the second level quickly and shrink running lanes for defenders in run support. While other teams are quick to spread teams out, the 49ers are more apt to sub to seven man “jumbo” line packages.

Defensively, the 49ers are ferocious. They possess difference-making, elite talent at every level of the defense. This talent surplus allows defensive coordinator Vic Fangio to run a rather simple scheme. Outside of line stunts and an occasional extra blitzer, the 49ers typically line up and beat teams man-to-man.

2011 All Pro Justin Smith is the lynch pin of the 49ers defensive line. Smith plays the run better than any 49ers defensive lineman. While he isn’t rushing the passer with the same success this season, he’s tireless on inside stunts and frequently occupies multiple blockers.

Outside linebackers in the 49ers scheme must first-and-foremost be able to rush the passer, and then be able to set the edge against the run. Second-year standout Aldon Smith is the complete package. Smith is an angular athlete who plays with leverage and is violent with his hands. His long arms provide him extra reach to keep blockers at bay, and allow him to finish plays in the backfield.

If you were to ask general managers who the best inside linebacker in the league is currently, it’s guaranteed that the top two vote-getters would be Patrick Willis and NaVorro Bowman. It’s not coincidental that the 49ers defense didn’t give up a 100-yard rusher for the first 30 games that these two started together. These two form the most formidable pair of second-level run defenders in the league.

By having such a dominant front seven, the 49ers secondary runs a variety of two-deep coverages. The 49ers run a lot of Cover-2 Man-Under — the defense that was overblown in the Bears-Packers game earlier this season, which I wrote about here. This coverage will allow them to bracket Brandon Marshall with extra help over the top.

Prior to the 2011 season, Baalke signed cornerback Carlos Rogers and safety Donte Whitner in free agency, completely reshaping the secondary. Rogers was signed to a one-year “prove it” deal, and he proved his value to the club. Rogers turned in a Pro Bowl, six interception season, which he parlayed into a four-year extension this off-season.

Homegrown safety Dashon Goldson has blossomed over the past few seasons. His versatility and range allows the 49ers to get creative at times with their scheme. Goldson is occasionally used as a “robber” in Cover-1 looks where he can patrol the underneath zone – similar to a Tampa-2 mike linebacker – to break up a pass or force a turnover.

The 49ers are one of the most well-rounded teams in the NFL, and are a legitimate Super Bowl contender. Even with deficiencies in the passing game, the 49ers coaching staff has schemed to its strengths on offense to move the ball and dominate time of possession. Defensively, the 49ers lead the NFL in the most important category, points allowed.

Both teams should err on the side of caution and sit their concussed quarterbacks. If that comes to pass, this game will come down to field position and turnovers. Even if these teams aren’t at full strength on Monday night, we could see them meet again in the NFC Championship game.

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Dan Durkin

Dan Durkin joined The Score’s columnist community after finishing runner-up in the 2011 Pepsi Max Score Search. He is a graduate of the University of Illinois where he was a member of the men’s football team (despite his best efforts to join the women’s team). Dan is a longtime Scorehead, known as Dan in Wicker Park – even though he no longer resides in Wicker Park – who will be sharing NFL analysis and opinions. You can follow Dan on Twitter @djdurkin. To read more of Dan’s blogs click here.

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