Grant Cohn: Kyle Shanahan called shots on 49ers’ hiring of John Lynch

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Jed York is experiencing growing pains which may develop into severe stomach? cramps. But first, let’s talk about John Lynch, the 49ers’ new general manager.

For all we know, Lynch may turn out to be a fantastic GM but, please, this is a stunning hire. And not in the good sense.

Lynch never has been a GM or a personnel executive or a scout. He has no background running a team or putting one together in any capacity. He has a background in broadcasting - has been a color commentator for Fox since 2008.

He also played in the NFL. He was a nine-time Pro-Bowl safety for the Buccaneers and Broncos, and he’s a future Hall of Famer. He played under Mike Shanahan in Denver, Jon Gruden in Tampa Bay and Bill Walsh at Stanford.

Lynch is extremely bright. He’s also close with John Elway, another Hall-of-Fame player who went to Stanford and became a GM. Elway runs the Broncos, and they won the Super Bowl last year.

It’s possible the Niners just hired the next Elway - an exciting thought for the 49ers and their fans. But the owner of the team doesn’t sound so excited.

After hiring Lynch on Sunday night, Jed York spoke with Peter King of Sports Illustrated, and told King, “We understand we’ll have to live with growing pains.”

Excuse me? Growing pains?

When I think of growing pains, I think of suffering, torment, torture, misery, agony. This is the language York used to introduce his new GM. Why would he use such negative imagery? Lynch hadn’t even yet had his opening press conference (he spoke to reporters on a conference call Monday afternoon), and York was lowering expectations.

What other owner would do that? Would Eddie DeBartolo Jr. do that?

Of course he wouldn’t. He or any sensible owner would say, “We are confident in John Lynch and thrilled he is our general manager. We are sure he will lead us to the Super Bowl.”

That’s positive, confident language, the right kind of language.

York sounds like he’s bracing for a terrible outcome and insulating himself from blame. Like he’s saying, “Look, we know we’re going to lose most of our games until this guy figures out what he’s doing.”

“Growing pains” implies a begrudging acceptance, as if York had no alternative but to hire Lynch and endure what comes next. As if Lynch was forced upon York by Kyle Shanahan, the offensive coordinator of the NFC-champion Falcons and almost certainly the next head coach of the 49ers.

Lynch admitted that Shanahan lobbied for him. “Kyle and I were in a conversation (about Lynch becoming the GM),” he said during his opening conference call. “(Shanahan) seemed excited at that point. He turned it over to Jed and Paraag (Marathe, 49ers executive vice president), and the rest moved fairly quickly.”

York admitted the same thing to King. “I talk to Kyle,” York said. “He says John is the most prepared of all the TV (people) he meets in the production meetings before games.”

Let’s skip over the ridiculous comment on production meetings and how they possibly can teach someone how to be a GM. What is York saying? He’s saying something like this: “Shanahan wanted Lynch. This is Shanahan’s guy. I had no choice. Don’t blame me if Lynch fails.”

I believe Shanahan insisted on hiring Lynch, made Lynch a last-minute stipulation, said Lynch is his guy or else. Said something like, “If you want me, you have to hire the GM of my choosing. Otherwise, I won’t be your head coach and you’ll have to find someone else. And good luck.”

Finding someone else would be almost impossible at this point in the offseason. All the other good head-coaching candidates have been hired already. Shanahan had York by the you-know-what.

That’s York’s fault. He put himself in that position by mishandling the GM search and head-coaching search from the beginning.

Instead of hiring a director of football operations to lead the search and conduct the interviews for him, York did everything himself along with Marathe - a numbers guy. Not a football guy.

According to Mike Florio of Pro Football Talk, York’s “first, second and third choice” for the GM job was former Chiefs executive Chris Ballard. But Ballard had no desire to sit for an interview with York and Marathe - something about that combo turned him off - so he asked the Chiefs to deny him permission to meet with the 49ers.

A couple weeks later, the Colts fired their GM and requested to interview Ballard, who jumped at the opportunity. Now, he’s the Colts’ GM.

Indianapolis hired York’s top target.

After getting turned down by Ballard, York requested permission to interview Patriots executive Nick Caserio, and he turned down York as well. Then York and Marathe met with four other executives - Eliot Wolf, Brian Gutekunst, Trent Kirchner and Scott Fitterer - and all of them turned down the 49ers after just one interview with York and Marathe. Something about that combo turned them off.

At this point, after waiting for these GM candidates only to get turned down by them, every qualified coach had been hired except one - Kyle Shanahan. Shanahan is an excellent offensive coordinator who is just 37 years old and never has been a head coach.

York made Shanahan the focus of the search. And in doing so, York gave Shanahan leverage in the negotiations, leverage Shanahan almost certainly used to hire Lynch, someone he can control.

All this means York ended up with a GM who has no bona fides, and a novice head coach who has a ton of power. York hired a couple of experiments. He’s back in the experimental phase, exactly where he was when he hired Mike Singletary, Jim Tomsula and Chip Kelly.

York is a terrible experimenter. He should be out of the experimenting business. He should have followed the proper protocol, hired a director of football operations, let him hire the GM and let the GM hire the head coach.

If York had followed protocol, he probably would have gotten Chris Ballard or Nick Caserio or Eliot Wolf - a GM with the chops to run the 49ers right now.

Instead, York got growing pains.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for The Press Democrat’s website. You can reach him at grantcohn@gmail.com.