CEO Jed York became familiar with the dynamics of managing years ago when the 49ers general manager and head coach were often pulling in different directions.
It was a part of life for York in dealing with executive Trent Baalke and head coaches Mike Singletary, Jim Harbaugh, Jim Tomsula and Chip Kelly.
“I’ve seen dysfunction before,” York said on 49ers Talk, “and I know what it looks like when two people are not on the same page.”
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York said he spent enough time with general manager John Lynch and coach Kyle Shanahan in the month before the draft to believe there was no substance to reports that suggested a division within the organization
“These guys were working toward getting to the right answer,” York said.
The 49ers on March 26 made the trade to move up to the No. 3 overall pick. After the expected selections of Trevor Lawrence and Zach Wilson with the Nos. 1 and 2 picks, the 49ers were considering three quarterbacks -- Trey Lance, Justin Fields and Mac Jones -- with the third pick.
Reports surfaced that Shanahan preferred Jones, while the personnel department was pushing Lance.
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York said he spent a great deal of time with Lynch and Shanahan during that time, and was impressed at how they reached a mutual decision. He also recognized that each man had a different process toward arriving at his personal preference.
“They came to their own decision jointly,” York said. “But as much jointly, independently of trying to get to the right answer of why they wanted to draft. I knew they would get there.”
Despite three losing seasons in the four years of the Lynch-Shanahan pairing, York said he has never wavered in his confidence and belief the two top football men in the organization will remain together for a long time.
Shanahan and Lynch came to the 49ers after a three-year span in which the 49ers had three different head coaches. In the 49ers' third year of Shanahan and Lynch, San Francisco advanced to the Super Bowl.
The 49ers dropped back to 6-10 during the 2020 season -- a year in which their depth chart was decimated by injuries to many of their top players, such as quarterback Jimmy Garoppolo, tight end George Kittle, defensive ends Nick Bosa and Dee Ford, and cornerback Richard Sherman.
Lynch and Shanahan arrived at the decision together that it was time to trade up for the quarterback of the future.
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York said he thought even the way Lynch and Shanahan communicated the decision to quarterback Garoppolo distinguishes them from many in the NFL.
“It could be a very sensitive situation, but I think we handled it differently than most other teams would, where we talked to our starting quarterback and let him know that we’re going to do this upfront,” York said.
“It’s not an easy conversation. It’s not a fun conversation. But I think those guys are always honest and always direct and I believe we will always have a chance to compete with those guys being here and being on the same page.”