After Mike Singletary laid the blueprint on how not to manage quarterbacks during his short stint in San Francisco, the 49ers’ next head coach had to be someone who knew how to develop that position.

As soon as they jettisoned Singletary in Week 16, they targeted Jim Harbaugh as their top choice. The work he did with Josh Johnson at the University of San Diego and likely future No. 1 overall pick Andrew Luck at Stanford was proof that he could effectively develop quarterbacks. The fact that Harbaugh didn’t have any experience as a NFL assistant didn’t matter because that wasn’t the Niners’ top priority. It would have helped, but it obviously wasn’t a deal breaker because the team agreed to terms with the former Stanford coach on a five-year, $25 million contract on Friday.

Harbaugh takes over a team that is certainly not short on talent. The Niners already have a top-13 defense and with players like Frank Gore, Vernon Davis and Michael Crabtree, the offense is in good shape, too.

But the one position that has held the 49ers back over the years has been quarterback. Whether it’s Alex Smith, Troy Smith or Shaun Hill, the quarterback position in San Francisco has been a black hole. Part of the blame falls on Singletary because he was overmatched as a head coach from the start. The fact that the team could never settle on an offensive coordinator didn’t help either. But Alex Smith has been the model of inconsistency. At times he’s shown that he has what it takes to succeed but he’s never taken that next step to become a reliable starter.

Now it’s up to Harbaugh to determine if he can work with Smith or if the team should go in another direction. At this point, it might be wise to clean house and start over, which I’m sure Harbaugh will consider. After all, why not try to win with your guy as opposed to someone elses?

Either way, Harbaugh was the right choice for this team all along and San Francisco was the right fit for him. There’s no guarantee that he’ll succeed and if history is any indication, he won’t because he was a highly sought after college coach. And maybe in a couple of years we’ll look back and say that he should have stayed in the college ranks and coached at his alma mater Michigan.

But at least right now, the deal works for all parties involved.

Jim Harbaugh continues to be one of the hottest names in football and if he wants to leave Stanford for a bigger job next season, he’ll likely have opportunities at both the college and pro level.

According to Matt Maiocco of Comcast SportsNet Bay Area, the 49ers are interested in Harbaugh as head-coaching replacement for Mike Singletary (who was fired on Monday). The Niners view Harbaugh’s work with Josh Johnson and NFL prospect Andrew Luck as a sign that he can develop quarterbacks. And seeing as how that was one of Singletary’s downfalls, they would love to secure a head coach who knows how to manage signal callers.

Maiocco also confirms that Trent Baalke will be promoted from V.P. of Player Personnel to General Manager. The team wanted to have a GM in place before they sought a head coach and now that they have one, you can expect them to start interviewing coaches once their season wraps up this Sunday (if not sooner).

One name I keep throwing onto the table is Jon Gruden, and for the same reasons the Niners like Harbaugh: he can work with quarterbacks. Gruden had success in the NFL with Rich Gannon, Brad Johnson and Jeff Garcia, so if San Fran is looking for a coach who knows QBs then “Chucky” may be the perfect fit.

That said, who knows if Gruden wants to come out of the booth right now. He enjoys working with the Monday Night Football crew and he may not be ready to return to the sidelines yet. But if he does, I don’t see why the Niners wouldn’t at least pick up the phone and gauge his interest in returning to the Bay area. Harbaugh would be a fine choice, but if San Fran is looking for more pro experience, then you can’t beat Gruden’s resume, which includes hoisting a Lombardi Trophy.