The 6′ 5″ frame of Colin Kaepernick looms over each of the many financial decisions the 49ers face this offseason. Whether it’s re-signing Anquan Boldin, Donte Whitner, Tarell Brown or Phil Dawson, Kaepernick’s contract status will directly affect the number of cap dollars available. When the team plans on how they’ll attack the 2014 NFL Draft, the players they keep from the 2013 team — plus those they add from other teams via free agency and/or trades — have to be considered.

All those decisions, plus the overall direction of the offense and the team at large, hinge on one thing: a potential extension for Kaepernick.

Why pay now?

What the extension would cost is almost irrelevant at this point. Every quarterback gets nine figures as far as the agent-approved, let’s-announce-this-and-create-a-big-stir contract is concerned. Whether it’s Matthew Stafford, Joe Flacco, Tony Romo, Jay Cutler or Kaepernick (all quarterbacks who are both talented and flawed), the guaranteed money will be large and the impact on a team’s cap will be substantial.

The 49ers have a year to decide whether to let Kaepernick play the season out while making a base salary of $973,766 with a cap hit of $1,630,454, or end all the questions now. Kevin Lynch of the San Francisco Chronicle explained what’s in it for the 49ers to lock Kaepernick up before he becomes an unrestricted free agent.

Here’s a solution. Kaepernick still has one year left on his rookie deal that pays him just over a million. So the 49ers could eliminate that final year and get Kaepernick the big money sooner – at a discount of course.

So instead of $18 million for five in 2015, how about $15 million for five in 2014? Kaepernick gets to be Imelda Marcos one year early and the deal is essentially the same because the woefully underpaid 2014 season is wiped out.

(The Imelda Marcos line is a joke about Kaepernick’s extensive sneaker collection that no one under 30 will get.)

Colin Kaepernick Jim Harbaugh 49ersAll in the family

The extension questions facing the 49ers — which also include Jim Harbaugh’s future with the organization — will shine some light on just how similar Jed York is to his uncle.

Harbaugh has been the driving force behind the 49ers’ current renaissance, and Kaepernick has led the 49ers to four playoff victories in two seasons.

However, the Harbaugh/Kaepernick partnership has yet to provide young Jed with a Super Bowl ring. York doesn’t seem nearly as volatile as Mr. D, but his stadium is already a done deal. Does he really want to foster the image that he and the team are simply grateful to once again be competitive? His uncle chased off Bill Walsh and traded Joe Montana. Harbaugh isn’t Walsh (just ask Lowell Cohn, he’ll hammer that point home again and again and again …), and Kaepernick doesn’t even have a decent quarterback waiting in the wings, never mind a guy like Steve Young.

After the difficulties York faced with his immediate family’s previous coaching hires, along with how coaches’ salaries don’t affect a team’s cap situation, it seems likely that they’ll talk to Harbaugh about a raise to put his salary in line with his peers. York has already approached Harbaugh about an extension before, but Harbaugh — who’d like to be the highest-paid coach in the NFL — has been willing in the past to let his contract play out until he wins a Super Bowl according to Tim Kawakami.

On the other hand, nothing has been said about Kaepernick.

I’ve heard from a source close to the team that they’re in a wait-and-see mode with Kaepernick, but that was before this season so things may have changed. However, one of the reasons Harbaugh rose through the coaching ranks so quickly and became such an attractive option for teams like the 49ers and Dolphins is his reputation as a “quarterback whisperer” of sorts. Harbaugh hates any sort of question that lends credence to this idea that he has some sort of magical ability to turn mediocre quarterbacks into good ones and good ones into elite signal callers, and one can probably assume Andrew Luck would’ve been a fantastic quarterback independent of where he played college ball. Yet, as crazy as it sounds, I can see how the 49ers might think it’d be easier to find a new quarterback than a new head coach who can groom quarterbacks as well as Harbaugh.

The 2014 NFL Draft

There are no free agent quarterbacks worth considering if the 49ers are looking for a future starter. If they’re thinking about either putting a little added pressure on Kaepernick or continuing in their current mode of skimping on the quarterback position (in a financial sense) in an effort to make putting together a powerhouse supporting cast easier, we’ll find out by the second day of the NFL Draft.

Colt McCoy is more of a placeholder than a suitable answer, and he’s a free agent anyway. McLeod Bethel-Thompson will compete to be the backup, but that’s as high as his ceiling goes. The more I consider the 49ers’ future options, the more I wonder if they might take a quarterback much earlier than anyone is currently projecting.

The 49ers have shown a willingness to gamble in the draft on gimmicky players (LaMichael James) and players who drop due to injury (Marcus Lattimore, Tank Carradine). Everyone knows they could use some reinforcements at cornerback, wide receiver, guard, center, and perhaps safety and inside linebacker as well. But if they trust in Harbaugh’s ability to develop quality quarterbacks in minimal time (and Harbaugh finds someone who he really likes that the 49ers won’t have to mortgage their future to select), maybe they try to find the next Kaepernick — a version who’s more accurate, and more willing to patiently go through his progressions and speak to the media in complete sentences.

(I’m kidding about that last part, although some members of the organization do wish Kaepernick would be a little more cooperative at times.)

Harbaugh compliments Kaepernick at every turn — as he did with Alex Smith — but there may be people in the front office who are wary of giving the biggest contract in franchise history (by far) to a quarterback whose best attribute is his legs. One knee injury could turn a big-money extension into a big disaster, despite Kaepernick’s powerful frame.

The Amici’s contest question

When 49ers fans aren’t watching commercials and bitching about Richard Sherman on Sunday, they might have a debate about the following question.

Should the 49ers sign Colin Kaepernick to a contract extension now, or should they wait a year and see what he can do in 2014? 

We’re giving away two 10-person pizza parties for Sunday’s game (I’m not sure if I’m allowed to mention the name of the game, so to be safe we’ll just call it “The Big Game where everyone around here roots for Peyton Manning for the first time ever”). Comment on this post and you’ll be entered to have your party catered by Amici’s East Coast Pizzeria. To give yourself a better chance at tons of free food for you and your friends, you can comment on the posts below as well.

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