After an improbable postseason that ended a game away from the Super Bowl, he will need an even better offseason if he wants the success to continue.
So far, he is on the right track. Re-signing all of his key defensive free-agents and bringing in two dynamic wide receivers (Randy Moss and Mario Manningham) almost ensures that the 49ers will be contenders next season.
With the NFL draft quickly approaching, the 49ers will have the opportunity to find the last missing pieces needed to make a Super Bowl run.
Given his familiarity with the Pacific Division, it would be no surprise if he selects a few prospects he coached with and against to solidify the roster.
This slideshow will highlight the Pac-12 standouts that would fit right into the 49ers' 2012 lineup.
The San Francisco 49ers were unable to re-sign their starting right guard Adam Snyder. This leaves a gap in an already leaky offensive line.
Enter David DeCastro.
The former Stanford Cardinal is one of the best guard prospects to enter the draft in recent memory. At 6'5" and 316 pounds, DeCastro promises to be a decade-long starter.
His rare combination of size, power and short-distance quickness is a rare commodity, one that will ensure that he is off the boards before the middle of the first round.
Jim Harbaugh has yet to sign a free agent guard to replace Snyder. Is this because he plans to trade up to get his former guard?
It would be a pricey move, but well worth the cost.
DeCastro is the perfect fit for the 49ers' ground-and-pound offense and will be a starter as soon as he is given a helmet.
Kendall Hunter looked promising in his rookie season, but the 5'7," 199-pounder cannot be trusted to carry the load.
Selecting Chris Polk would ensure that the San Francisco 49ers' run game does not lose a beat once Gore's resilient tires finally fall off.
In the last three seasons, Polk gained a total of 4,016 yards and averaged over five yards per carry. Not to mention he caught at least 22 passes every season over the same span.
The 49ers' offense is not desperate for a starting running back right now, but they will be as soon as Gore's productive career comes to a halt (I give him one more season).
Polk has the potential to fill the do-everything role Gore has had since becoming the starter in 2006. With Hunter as the change-of-pace back, the 49ers' ground game will continue to thrive even when Gore is out of the picture.
The San Francisco 49ers have suffered from a lack of playmakers for too long.
Jim Harbaugh finally did something about it this offseason when he added Randy Moss and Mario Manningham via free agency.
Considering that the 49ers already have Michael Crabtree, Vernon Davis and Delaine Walker, it may seem as though their receiver woes are a thing of the past, but they are not.
Moss was out of the league last season, and Manningham was the third receiver on the New York Giants' depth chart the last few years. While both of these players have tremendous upside, you never know how they will fit into a new offense.
Adding Coby Fleener would ensure that the 49ers' offense reaches the next level in 2012.
At 6'6" and 247 pounds, Fleener has the perfect frame to become a dominant red zone threat. The combination of his long arms and height will make him impossible to contain in jump ball situations.
If he fulfills his potential, his Jimmy Graham-like frame would demand a double team. With Davis and Moss already earning extra attention, defenses simply would not be able to eliminate Alex Smith's options.
Isaac Sopoaga, Ray McDonald and Justin Smith made up one of the most dominant 3-4 fronts in the NFL last season. But behind them, the San Francisco 49ers have nothing.
Adding depth to the defensive line has to be one of the 49ers' top priorities in the draft.
Backups Ricky Jean-Francois, Ian Williams and Will Tukuafu are the only reserves and none of them have proven themselves to be trustful backups.
DaJohn Harris is a strong prospect coming out of Southern California. At 6'3" and 306 pounds, he is the ideal size for a 3-4 defensive end. His collegiate career was marred by inconsistencies, but his athleticism is undeniable.
At best, Harris is a three-down defensive lineman with the ability to clog the run and pressure the quarterback.
At worst, Harris will come up empty on the stat sheet and raise questions about his durability.
Because of his inability to dominate in college, Harris will be around in the fourth round should the 49ers be interested.
Harris has the potential to be a late bloomer. If he puts in the correct amount of time and effort, he could see time as a rookie in a backup role before pushing for the starting spot once the 32-year-old Smith retires.
As previously mentioned, the San Francisco 49ers need depth on the defensive line, more specifically at nose tackle.
Besides for Isaac Sopoaga and Ian Williams (who hardly saw the field in 2011), the 49ers do not have a defensive linemen that weighs over 300 pounds.
Ta'amu is 347 pounds and appears to have been bred to play nose tackle.
He is pretty much a non-factor as a pass-rusher but can be effective against the run early on in his career.
As a rookie, Ta'amu could rotate with Sopoaga on run downs. His ability to neutralize offensive lineman will allow Patrick Willis and NaVorro Bowman to roam freely in the box and make plays.
Ta'amu has a high ceiling if he can improve his conditioning and pass-rush abilities. Regardless, he is a great mid-round pickup who can contribute immediately.
With the additions of Randy Moss and Mario Manningham, receiver is no longer a position of need.
But once Moss is gone (he only signed a one-year deal), the San Francisco 49ers' receiving corp will be without a tall receiver, one that can dominate in the red zone.
Gerell Robinson is an overlooked prospect from Arizona State. He is not a burner (4.63 second 40-yard dash at the NFL combine), but he is incredibly physical and has sure hands.
In college, Robinson thrived running intermediate routes over the middle. He is not afraid of contact and has a knack for securing the ball just before defenders dish out the big hit.
Robinson has the potential to be the same type of consistent receiver the 49ers had in Josh Morgan. The only difference is that Robinson is taller, stronger and a better red-zone target.
Due to the abundance of tall, physical receivers in this year's draft class, Robinson will be available on the third day of the draft, making him the ultimate value pick.
Vontaze Burfict's character flaws have been widely publicized. At the rate he is going, he may go down as one of the biggest wasted talents in pro sports history.
Following the 2011 season, he was pegged as a sure first-rounder. But following a horrendous combine and pro day, he may not even get drafted.
Should he fall as far as the seventh round, the San Francisco 49ers should pick him up.
He will most likely be nothing more than a cancerous addition to a locker room that already has two stud middle linebackers (Patrick Willis and NaVorro Bowman, aka Boom-Boom and Bam-Bam). But as a seventh-round pick, he is worth the risk.
Assuming that Burfict does not figure out that the only thing holding him back is himself, he can be cut during the preseason and the whole matter will be forgotten; most seventh-rounders get cut around this time anyways.
On the off chance that he responds to Jim Harbaugh and the coaching staff, he could be special.
At his best, Burfict is a ferocious tackler and will instill fear in opposing offenses. He is also a more natural pass-rusher than Willis and could even make the transition to outside linebacker.
Considering that Harbaugh drafted a defensive end in the seventh round last year and transformed him into a solid fullback, there is no reason to doubt that he can turn the frumpy Burfict into a happy-go-lucky quarterback killer.