There was one impossible-to-miss-takeaway from Jed York’s interview in Arizona on Friday: The 49ers’ owner believes his revamped coaching staff will do a better job of putting players in a “position to make plays.”

York used some variation of that nebulous phrase on five occasions during the course of his seven-minute interview on NFL Network from the site of Sunday’s Super Bowl. So what exactly does that mean? York came closest to getting specific when he suggested the 49ers plan to allow dual-threat quarterback Colin Kaepernick to make more plays with his feet in 2015.

“You’ve got a great guy in (quarterbacks coach) Steve Logan that’s coming in that’s going to work with him on fundamentals and allow us to put together a system that’s going to put Kap in the best position to make plays,” York said. “How many quarterbacks in this league can run 90 yards for a touchdown? I can’t think of many.

“But you’ve got to put Kap in a position where he can make those plays. And put Kap in a position where we can run the ball.”

In 2014, his second full season as a starter, Kaepernick rushed for a career-high 639 yards and averaged 6.1 yards a carry. In an overtime loss to the Chargers on Dec. 20, he rushed for 151 yards on seven carries and his 90-yard touchdown run was the second-longest scamper by a quarterback in NFL history.

In an effort to keep Kaepernick healthy, the 49ers have typically avoided having him run too much in the regular season, but have turned him loose in the playoffs. Three of the top rushing performances of Kaepernick’s career have come in his six postseason starts. He’s averaged 84.5 rushing yards in the playoffs, and 35.9 yards in 39 regular-season starts.

“We can throw the ball in ways that allow him to be successful, and let him be the absolute stud that he can be on the field.” York said. “And I think that’s what you’re going to see from us next year. Defenses are not going to want to play against us because you’re not going to know where we’re going to hit you.”

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Many fans are less bullish on the 49ers’ upcoming season after head coach Jim Harbaugh was replaced by defensive line coach Jim Tomsula, defensive coordinator Vic Fangio’s role was assumed by tight ends coach Eric Mangini and offensive coordinator Greg Roman was replaced by quarterbacks coach Geep Chryst.

York noted that Mangini and Chryst, who was promoted after the 49ers pursued several other offensive-coordinator candidates, were hired by Harbaugh.

“I think that’s a testament to Jim Harbaugh that we are keeping a lot of continuity from his staff that’s had a lot of success,” York said, later adding: “I think we’re going in a direction that continues a lot of the things that (Harbaugh) helped put in place. And we’re going to take it to the next step. And I’m very excited about where we are.”

So, if continuity from a staff that helped lead the 49ers to a 44-19-1 record since 2011 is a selling point, why is the staff’s leader, Harbaugh, now Michigan’s head coach?

York, again, downplayed the notion that the parting with Harbaugh was inspired by a personality conflict.

“When you mutually part ways there are two sides to it,” York said. “I realize people don’t want to look at it like that — they want to say Jim was fired. That’s not the case. Jim signed on at Michigan very shortly after he left. Obviously, there were announcements before he left that he was going to Michigan and he obviously had a tie to his alma mater. There were things there — it wasn’t, 'Well, we just couldn’t get along.’ It was on both sides.”

Eric Branch is a San Francisco Chronicle staff writer. E-mail: ebranch@sfchronicle.com. Twitter: @Eric_Branch