So now we know why the 49ers aren’t spending much on free agents: Jed York hasn’t paid the rent.

In Negative Headline No. 1,623 since the team left San Francisco and moved into the haunted house that is Levi’s Stadium — sometimes karma doesn’t suck — new Santa Clara mayor Lisa Gillmor says the Niners are $5.5 million short on annual rent payments. Naturally, York’s people say the current demands have been satisfied and that they’re seeking a rent reduction. Still, if the city is expecting $24.5 million and has collected only $19 million, it’s akin to a techie paying only $2,800 for his mid-Market studio when he owes his monthly $3,500.

Meaning, Jed soon could arrive to work with an eviction notice on the door at 4949 Marie DeBartolo Drive. For stadium options, he should know Candlestick Park is a heaping pile of rubble, Mark Davis would agree to restyle his bowlcut hair before letting the Niners share O.co Coliseum with the Raiders, and adorable Kezar Stadium seats only 10,000 in its current iteration — not that the 49ers have half that many fans these days.

Tell me, Jared Goff: Do you really want to play for these flim-flam fools?

“Growing up as a fan of them, that would be awesome,” he said after his Pro Day workout at Cal, before wisely adding, “But at the same time, I’d be more than happy to play anywhere and be with a team or a coach that I want to win games with or be very successful with.”

In an absurdist debacle that has become typical of York’s franchise, the 49ers have followed a dysfunctional 2015 with a chaotic offseason. With Goff, the talented quarterback prospect from Marin, available high in the first round of the upcoming draft, they at least have a chance with the seventh overall pick to provide a hopeful, compelling story line. But 11 years after the York family rejected a Cal QB named Aaron Rodgers, why do I see a scenario where the 49ers don’t pursue Goff and then watch him enjoy a fabulous career elsewhere?

Clad in a pullover and cap, Chip Kelly showed up in Berkeley for the high-profile, nationally televised showcase, yet chatted only briefly with Goff. He continues to voice a bizarre hankering for Colin Kaepernick in what’s looming as a classic disconnect between a new coach, the wacky front office and a disgruntled QB who has aggressively demanded a trade. You remember when Kaepernick ripped Donald Trump for the anti-Muslim climate in America, writing on Instagram, “Racism and discrimination isn’t OK. We’re all human beings! Things need to change!” Seems he might prefer voting for Trump than returning to a franchise he doesn’t trust, starting with CEO York and general manager Trent Baalke.

Yet Kelly isn’t grasping reality. “I’d love to have him. I’m a big Kap fan. I talked to Kap two days ago. It was a good conversation,” he said last week. “I told him, ‘If you’re here, we are going to coach you.’” All while York and Baalke are trying to squeeze a second- or third-round draft pick for Kaepernick on the trade market, while Denver Broncos football boss John Elway — whose chances you like in any staredown with Jed and Trent — views Kaepernick as worthy of fourth-round value. This could go on quite a while, with Cleveland and the New York Jets also involved, but the longer the standoff lasts, the more embarrassing and harmful the situation becomes for the 49ers. If a trade isn’t consummated by April Fools Day, Kaepernick’s $11.9 million base salary is guaranteed, after which he’ll surely blow off the April 4 start of team activities … and create Negative Headline No. 1,624.

What’s crazier is, Kaepernick has regressed so woefully since the team move to Levi’s — or since Jed and Trent turned on Jim Harbaugh, the coach who created the once-revolutionary Kaepernick — that the 49ers should ache to start anew with a project like Goff. Or, if he were to fall to them on draft night, Carson Wentz. Developing young QBs is what Kelly does, right? York has said the new coach will be here “for a long time,” so if Kelly likes what he sees in Goff or Wentz, he has the job security to make a major play for a major prospect and build the 49ers around him. Trying to make amends with Kaepernick, a locker room distraction who isn’t accurate enough as a passer to succeed in Kelly’s quick-tempo offense, makes about as much sense as, well, stiffing the city of Santa Clara on rent money.

Scarier is the idea of putting the franchise’s future in the unqualified mitts of Baalke. After whiffing on the entire 2012 draft and missing badly since then, he’s among the NFL’s worst talent evaluators. Do you really want him pulling the trigger on 12 picks next month? He really should use some of those picks to trade up with the Tennessee Titans, land the top selection and make damn sure they have a QB for Kelly to work with. Will Trent have the wherewithal? You already know that answer.

In a division with two ongoing Super Bowl contenders (Seattle and Arizona) and the Los Angeles-rejuvenated Rams, the 49ers may not be a serious operation for years. That should be more evident based on their lack of impact in free agency. Other than giving $11.75 million to guard Zane Beadles to replace departed Alex Boone and throwing a few pennies at backup QB Thad Lewis, Jed and Trent have been quiet. What happened to all that promising talk about having more than $60 million in salary-cap space? Again, Kelly is trying to be a public buffer for his bumbling bosses, blaming a mediocre player pool in saying, “You’re going to pay some guy who’s never made a Pro Bowl who’s going to make more than anybody on your roster — that’s a little bit difficult.”

So, where does the rest of the $60 million go?

Not to the rent payment, obviously.

Jay Mariotti is sports director and lead sports columnist at the San Francisco Examiner. He can be reached at jmariotti@sfexaminer.com. Read his website at jaymariotti.com.

Jay Mariotti

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