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Niners need to get out the checkbook

49ers

The bad news for the 49ers is that their season has ended one step short of the Super Bowl. The worse news is that the 49ers now have to start rewarding financially those who have helped the team make it to three straight NFC title games.

It’s a given that the 49ers will try to extend the contract of coach Jim Harbaugh. The question is whether he’ll look to break the bank with an eight-figure annual payday -- or at a minimum to do better than his brother, John, who’s making $7 million annually in Baltimore. If Harbaugh aims higher than the Niners are willing to go, it wouldn’t be a surprise if he decides to push toward coaching free agency after 2015.

Regardless of what the 49ers pay Harbaugh, they won’t have to count his money against the salary cap. Not so for players who are now due to be paid. Quarterback Colin Kaepernick leads the way, with the third year of his rookie second-round deal completed.

But what will he be worth? If he’d stepped up and delivered in the fourth quarter of Sunday’s game at Seattle, Kaepernick may have landed in the $18 million annual atmosphere. With a year left on his rookie deal, the challenge becomes putting a value on him right now that will reflect not only what he has done, but what he will do moving forward.

Receiver Michael Crabtree may think it’s time to get a new deal, too. He has played five years of a six-year, first-round deal from 2009. Due to earn a base salary of $3.5 million in 2014, Crabtree can make a strong case that he is underpaid.

Crabtree isn’t the only receiver who’ll want to be compensated. Anquan Boldin’s contract has expired, a year after the 49ers picked up the last year of it via a trade with the Ravens. If the 49ers let him go, good luck replacing his production and leadership.

And what about Aldon Smith? The seventh overall pick in 2011 didn’t receive a top-10 windfall, thanks to the rookie wage scale. While off-field issues have created a presumption that the 49ers will opt to wait, Smith’s performances can’t be denied. Apart from two sacks on Sunday in Seattle and 1.5 two weeks earlier in Green Bay, Smith has 42 sacks in 43 career regular-season games.

If the 49ers are worried about a suspension or other issues that would keep him away from the field for an extended stretch (again), the contract can be structured in a way that protects the team. The non-football issues also could help the 49ers get a good deal on a long-term contract, and in turn to give Smith a clear financial incentive to avoid future problems.

Regardless, the 49ers have some problems to address. Some may say they are good problems to have. The problems would be a lot better if they still had one more game to play this season.