Jim HarbaughThe 49ers have grown into one of the NFL’s few perennial powerhouses since Jim Harbaugh took over in 2011, and the head coach may be looking for even more control over his team.

Harbaugh has led the 49ers to a 32-11-1 record during his three seasons in San Francisco, including two trips to the NFC Championship Game and but a few yards from the franchise’s sixth Super Bowl trophy. His success is largely unparalleled in league history, at least for coaches in their first three seasons, and he’s even angling for another shot at the Lombardi Trophy again this season. Even with all the success and a young core in place, Harbaugh’s future in San Franciso isn’t exactly a given.

Harbaugh is something of a control freak. He knows what he wants. He knows what works. And he wants to be in control of the entire picture, not just the on-field elements. A big roadblock stands in his way of that goal, though, and it comes in the form of general manager Trent Baalke.

Baalke and Harbaugh reportedly have “creative tension” that stems from their differing opinions on the direction of the team — specifically personnel decisions — according to Tim Kawakami of the San Jose Mercury News. Those tensions have bubbled over at times, even subtly in a public forum, as Harbaugh has openly lobbied to bring back certain players, including safety Dashon Goldson, who signed with the Buccaneers during the offseason, and more recently kicker Phil Dawson, who is on a one-year deal. So, while Harbaugh and team owner Jed York get set to haggle out terms of a potential extension this offseason, more input into personnel decisions might be among his top priorities.

Harbaugh is currently in the third season of the five-year, $25 million deal that he signed when leaving Stanford in 2011. The $5 million salary seemed like a good chunk of change at the time, considering it more than tripled his salary at Stanford (reportedly $1.25 million) and because of his lack of NFL coaching experience, but, given his success, it now seems like a slap in the face when guys like Bill Belichick, Andy Reid and Pete Carroll are making upward of $7 million per season.

York has said openly that he plans to sit down with Harbaugh to discuss an extension this offseason, which seems promising. However, reports linking Harbaugh to the opening at the University of Texas might have York at least slightly concerned about hanging onto the head coach. And, in his quest for more power within the organization, Harbaugh’s best play is to welcome all the rumors and speculation and use it to his advantage.

Harbaugh already has the leverage of the past two seasons behind him in negotiations — he even turned down an extension offer during the offseason — and speculation about a move would only add to his power entering talks with York. He was smart to dodge questions about his rumored connection with the Longhorns’ opening, creating the illusion that, while he’s not actively pursuing it, he’s not entirely uninterested.

The idea of Harbaugh leaving at all should frighten the Niners enough to not only make him one of the highest-paid coaches in the league, but to also offer him the creative control he seeks. That doesn’t mean that York should can Baalke in favor of Harbaugh, as the GM has played a crucial role in building this team as well, but he should at least be willing to offer his coach some extra say into the players he’ll be coaching.

It seems pretty far-fetched to think that Harbaugh would ever leave the NFL for another college job — even somewhere with as much tradition and resources as Texas. That doesn’t mean it couldn’t happen, though, and Harbaugh would be wise to play up that possibility. He clearly has thoughts and plans for the 49ers’ future, and he wants the power to see them through. Fortunately, this is the right time, and he’s in the perfect situation, to bargain for that power.

Now, it just becomes a high-stakes game of poker between York and Harbaugh, and the coach has a full house just waiting on the river.

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