New regime shifts to offense on 3rd day

After the 49ers used their first three draft picks on defensive players, general manager and former NFL safety John Lynch was asked Friday about how his offensive-minded head coach was feeling.

Did Kyle Shanahan want to wrest control of the draft room?

“Yeah,” Lynch said, smiling. “We were just joking. He said, ‘All right, we’re going offense now. You’ve had your fun.’ ” Maybe they weren’t joking? Shortly after Lynch spoke, the 49ers traded up into the third round Friday to select Iowa quarterback C.J. Beathard, a move that set the tone for the final four rounds Saturday.

The 49ers opened by selecting Utah running back Joe Williams in the fourth round and grabbed Iowa tight end George Kittle and Louisiana Tech wide receiver Trent Taylor in the fifth. Before those selections, they acquired Broncos reserve running back Kapri Bibbs in a trade that included draft picks. Happy, Kyle? The offensive flurry began when the 49ers traded with the Colts to move up 22 spots and grab Williams.

In nine games last year, Williams, who ran a 4.41 40-yard dash, rushed for 1,407 yards (6.7 yards a carry) and 10 TDs.

It was quite a finish after Williams temporarily retired before the start of his senior season and missed four games, citing the mental and physical toll of football. He later said there were psychological reasons for stepping away.

Williams said he left football to finally deal with the emotional fallout from the death of his younger sister, Kylee, who had died at 7 in 2006 because of an undiagnosed heart problem. Kylee fell out of her bed at night and Williams blamed himself for not acting faster to save her.

“It was the guilt and the shame that I put upon myself because I didn’t act quickly enough, or wake my parents up or call 911,” Williams said. “I always thought it was my fault.”

Lynch said he initially dismissed the idea of drafting Williams because he was put off by the idea that he had “quit the team.” But Shanahan, after being wowed by Williams’ video, thought they should further investigate Williams’ story. Shanahan, running backs coach Bobby Turner and vice president of player personnel Adam Peters spoke extensively with Williams. Finally, on Saturday morning, before the draft, Lynch spoke with him.

“He just mentioned to me that throughout that process he addressed some things that had been bothering him for a long time,” Lynch said. “And he feels like he came out a different person. I think it’s a wonderful story.”

The 49ers selected Kittle during a draft in which they were speaking to teams about trading tight end Vance McDonald, a 2013 second-round pick who signed a five-year extension in December, when Trent Baalke was the general manager.

“I think that’s the reality of new regimes coming in, new schemes,” Lynch said. “That’s not to say he can’t fit into our scheme.”

Shanahan, who has been in touch with McDonald about the trade talks, said “a lot of people were interested” and the 49ers viewed it as an opportunity to upgrade in other areas.

“We took over a 2-14 team and we’re going to try to get better in every aspect,” Shanahan said. “… It’s not at all about not having a role. It’s about how can you improve your team.

Kittle is regarded as one of the draft’s best blocking tight ends. He had 42 catches for 604 yards and 10 touchdowns in his final two seasons, indicating his potential as a pass-catcher. He had the third-fastest 40-yard dash among tight ends at the combine (4.52 seconds).

“I put my team before anything that I wanted to do,” Kittle said. “I’m a person that could care less about stats. I just care about winning games.”

Taylor, 5-foot-8, is a slot receiver and punt returner who finished ranked third in the FBS among active career leaders in receptions (327) and fourth in receiving yards (4,179). Last year, he led the nation in receiving yards (1,803) and ranked second in receptions (136).

Taylor said he’s routinely been likened to a host of diminutive NFL receivers.

“I always get comparisons of all the slot guys, like (Wes) Welker, (Dallas’ Cole) Beasley, (New England’s Julian) Edelman,” Taylor said. “That’s what I’ve heard my whole life. But I’d like to go into the NFL and just be my own guy.” Eric Branch is a San Francisco Chronicle staff writer. Email: ebranch@sfchronicle.com Twitter: @Eric_Branch