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This whole thing — who will play quarterback for the 49ers next season — is all about Jim Harbaugh. It is not about Peyton Manning, who won't be playing in San Francisco.

And it is not even about Alex Smith, who may or may not be playing in San Francisco.

It is about Harbaugh, pure and simple. And right now he gets a failing grade.

Before I get into Harbaugh's performance, let's make something perfectly clear. Now that Manning is with Denver — appears to be — Smith is the 49ers' best quarterback option. Don't delude yourself that someone else can do better than this flawed quarterback — we know all about that. Smith did, after all, take the Niners to the NFC title game.

Don't delude yourself that Josh Johnson is the answer because he played for Harbaugh at the University of San Diego. Johnson is a nonentity.

And don't delude yourself that Colin Kaepernick is the answer. He is not, not at this time. He has virtually no experience in the NFL and he hasn't played a real game in two years.

In three years, he will be the 49ers quarterback if things go according to a prudent schedule, but he is not ready for the warp speed of NFL games and he will not take the Niners where they need to go next season. And Alex Smith just might.

If Harbaugh thinks otherwise, if he thinks he is so brilliant that the quarterback does not matter, he is allowing his ego to cloud his view of reality and he's falling into the old coach's trap that scheme is more important than players. Jimmy Johnson used to find that idea laughable.

"It's not Xs and Os," he said. "It's Jimmys and Joes."

That quote is especially relevant to the 49ers. Bill Walsh was nowhere until he got his own Joe — Joe Montana. If Harbaugh thinks Johnson or Kaepernick will get his team into the championship game, he is making the Steve DeBerg mistake — DeBerg was the forgettable Niner quarterback who preceded Montana.

OK, back to Harbaugh. He didn't get Manning, I believe, because of who he is.

Here is what David Cutliffe, head football coach at Duke and Manning's former coach at the University of Tennessee, told NFL Network: "For Peyton Manning to be Peyton Manning, you (coaches) have to lose a little bit of your ego and identity. The quarterbacks are always the functional part. We're (just) there to train them, but we're not taking snaps.

"You have to let Peyton Manning be Peyton Manning. That's when he's at his best. He's in control at the line of scrimmage. I think he needs a certain amount of autonomy because that's how he plays football. He played that way at the University of Tennessee, I'll be the first to admit that. I want every quarterback to know more than I do and I think that's how Peyton Manning does best."

Manning's coach has to lose a little bit of his ego. But it would be impossible for Harbaugh to lose his ego, to back up enough to let Manning be Manning.

Manning working with Harbaugh would have been a battle of wills, and Manning saw that and was wise to choose Denver. Harbaugh never had enough self-knowledge to know the truth because he is incapable of seeing life through someone else's eyes.

He can redeem himself right now, but this would require being the un-Harbaugh, learning flexibility and a little charm. He needs to court Smith and woo him back to the 49ers. He needs to do better with Smith than he did with Manning.

He must speak to Smith — maybe he has already — and say the pursuit of Manning was not personal. It was a business decision. A first-class organization in quest of a Super Bowl could not NOT go after Manning, a first-ballot Hall of Famer. The Niners owed it to themselves.

And then Harbaugh needs to tell Smith, "Let's get down to business. We want you. We believe in you." Harbaugh must show Smith respect even if Smith is savvy enough to understand why Harbaugh wanted Manning.

And then Harbaugh and general manager Trent Baalke need to offer Smith a better contract. They were talking about three years for $24 million. Seattle just gave Matt Flynn three years at $26 million with $10 million guaranteed — it is not known how much of the Niners' offer to Smith was guaranteed.

Well, Flynn started one game last season for the Packers. One game? He may have unlimited potential, but Smith has a copious body of work and he is worth more than Flynn to a contender. Let the Niners demonstrate his worth by improving their offer. They played their Manning card and lost. Right now, Smith has all the leverage, even though the Dolphins signed David Garrard on Monday. Miami may still consider signing Smith.

Whatever happens next is all about Harbaugh and his sincerity and his persuasiveness. Walsh could have pulled this off. This negotiation is more important to Harbaugh's career than any game plan he ever created or any game he ever coached.

Can he deliver?

For more on the world of sports in general and the Bay Area in particular, go to the Cohn Zohn at cohn.blogs.pressdemocrat.com. You can reach Staff Columnist Lowell Cohn at lowell.cohn@pressdemocrat.com.