SANTA CLARA, Calif. -- Colin Kaepernick downplayed the 49ers' clock-management issues as "minor" blips in their overall methodology on Wednesday, a day after his coach likened the process to a well-played game of chess.
But for a team that has suffered from time management troubles dating back beyond the crucial final drive of last February's Super Bowl, it has to be a growing concern.
"You're doing a lot of other good things right if that's the thing that worries (people) the most," coach Jim Harbaugh told KNBR on Tuesday.
In Sunday's 33-14 win at Tampa Bay, the 49ers spent a timeout and drew a delay-of-game penalty on their opening drive, foibles that ultimately didn't prevent a touchdown. Another timeout was lost just before that drive, when Harbaugh failed to win a replay challenge. (His sixth fail in eight review tries this season.)
On KNBR, Harbaugh likened timeout usage to a chess move, saying, "If you sacrificed a pawn to get the other person's queen, would that be a good trade?"
Kaepernick echoed that view Wednesday: "I know conventionally people are going to be like, 'Why are you taking a timeout at the beginning of the third quarter?' Well, if we sustain that drive and we end up with points at the end of that, we feel like that's a good timeout used."
As the clock wound down at the Superdome in February, with a third-down play called for Kaepernick to run it in from inside the Ravens' 10-yard-line, Harbaugh had to hurriedly call a timeout before the 49ers drew a delay-of-game penalty. San Francisco changed the play, and two end zone incompletions intended for Michael Crabtree later, the Ravens had a 34-31 victory.
"Felt the clock was grinding down and weren't going to get it off," Harbaugh said afterward.
According to Kaepernick, the flip side of that equation doesn't get enough emphasis. He noted that running the clock all the way down has its schematic advantages.
"If we snap the ball with one second, that's not a problem to us," he said. "Because we know we're getting to something we like versus their defense."
Now 24 starts into his career, Kaepernick said he feels comfortable not only digesting and relaying play calls but also keeping an eye on the play clock. "I'm pretty good as far as knowing, 'All right, I'll be able to get this off with a second or two left,"' he said.
But Kaepernick has drawn six delay-of game penalties this season. He had four last season, as did his predecessor, Alex Smith. Two more delay-of-game penalties came in last season's NFC Championship game win at Atlanta.
What must happen in the span of 40 seconds is clearly complicated: Harbaugh radios in a call, Kaepernick relays it in the huddle and often reiterates it to confused players exiting the huddle, then the young quarterback must analyze the defense and make any audible adjustments before the snap.
"There are times when you get to the point you're just running out of time to get to what you want to," Kaepernick said.
And if everyone is on the same page with the complex terminology, it could easily result in a "blown play."
"We have the feeling if we take the timeout to get something right and we end up getting points out of it, that's a beneficial timeout for us, whether it's early in the game, late in the game," Kaepernick said. "Regardless, if we end up with points out of that timeout, we feel like that's a good timeout used."
-- Harbaugh and general manager Trent Baalke coexist just fine in a dynamic where they "butt heads" and "sit down and argue things out," according to their boss, 49ers CEO Jed York. In an interview with KNBR, York said Harbaugh has never asked for personnel control three seasons into a five-year, $25 million deal.
"Now do we butt heads on players from time to time? Of course. That's what G.M.s and coaches do," York said. "But Jim knows that being a coach is a full-time job, and he has a lot of respect for the job that Trent has done."
Baalke has overseen the 49ers' personnel since 2010, and he received a contract extension in February 2012 that runs through 2016. Columnist Tim Kawakami reported Tuesday in this newspaper about tension that's apparently developed between Baalke and Harbaugh regarding personnel.
"They sit down and argue things out. And then they figure out: what's the best thing for the 49ers and let's move forward," York added. "And that's really how I see this team operating in the future and in perpetuity."
York anticipates sitting down with Harbaugh at season's end to hammer out a long-term extension, adding: "I definitely anticipate Jim being here for a long period of time."
-- Will Tukuafu, waived three months ago with a knee injury, re-signed Wednesday to help replace injured fullback Bruce Miller, who was placed on season-ending injured reserve with a fractured left scapula. Tukuafu split time last season on the defensive line and at fullback, albeit in a limited role on short-yardage and goal-line situations.
Anthony Dixon expects to get first crack at assuming Miller's role, including serving as Frank Gore's lead blocker. "I already know what (Gore) is looking for. I'm just looking to be physical," Dixon said.
-- Phil Dawson said he'd like to return to the 49ers next season, echoing Harbaugh's request Monday to re-sign the red-hot kicker. "It would be a tremendous opportunity to remain a 49er," Dawson said. "But right now, it's about the job at hand. Let's beat the Falcons, let's win our last game in Candlestick Park, let's secure our playoff spot."
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