Beyond personnel and schemes, how might the 49ers improve during the 2013 season?

Consider two non-plays from last year's Super Bowl. On the 49ers' first series, they hit on a pass downfield for a first down. However, because the play clock had expired, a penalty erased the gain, disrupted the 49er offensive flow, and probably altered subsequent play calling. Later, during the failed fourth-quarter goal-line assault, the Niners had, initially, the perfect play called, a high-conviction run that held promise as it got under way, with the blockers seemingly set up at advantageous angles. However the 49ers nipped that play, post-snap, in its nascent bud, calling time out, as per their regular-season pattern, because the play clock neared zero.

No doubt Kaepernick has worked hard this offseason to master the nuances of reading defenses, wrangling huddles, and making at-the-line adjustments, including pre-snap reads and audibles. And maybe Mangini can work with the staff to accelerate the play-calling or even help to install more time-friendly quick-huddle alternatives. Surely Coach Harbaugh, in his own sweet way, has addressed the problem.

The value of timeouts depends on individual game situations, but some teams often fall into the habit of calling timeouts willy-nilly just because of confusion in the huddle or too few or many players on the field. Obviously, if you trail by a touchdown with fourth-and-one at the opponent's nine-yard line and have eighteen seconds left, you want to call that timeout. The point is, you want to have that timeout to call, and maybe two more, should you make a first down; you do not want to have previously squandered them.

How squandered? Say you send your punt team out to kick from your opponent's forty-yard line. Your punter counts only nine teammates on the field. Probably better to take the five-yard penalty rather than waste a timeout. (Your opponent may decline it anyway, depending on down and distance, if you have an accomplished out-of-bounds punter.) Or say you have third and twenty from your own forty and intend to run a draw and then punt. The play clock ticks down. This one's not as clear cut, and depends also on the score, time remaining, strengths/weaknesses of both teams, and timeouts remaining. Ideally, you want to have previously weighed taking the five-yard penalty, versus the value of that timeout, before merely making the Pavlovian response by calling it.

Old-school coaches hate to give up even a scintilla of field position. They would rather hoard yardage than timeouts. But today's high-octane, quick-strike NFL offenses render timeouts even more important than in the ball-control era. Coaches also worry that a team in disarray might more likely make big mistakes, a legitimate concern. But probably not every occasion demands an automatic, pre-programmed timeout.

On first down of a scoreless game at midfield a back sweeps right, turns the corner near the sideline, plants his right foot, and launches himself forward for a six-yard gain. The hometown crowd applauds. Announcers gush. Coaches beam. Except an official overrules the play, claiming the plant foot was out of bounds. Three-yard gain. The offensive team's coach grabs for his red challenge flag, nervously fingers it while he consults with the coaches upstairs. Meanwhile, screens at home and in the stands show multiple replays. The play is close, close as upper-deck cheap seats. The announcers, after much discussion, conclude that the back's right foot, in fact, remained in bounds before the launch. The booth coaches, independently, agree. But it's close, very close. The head coach throws the challenge flag. The referee repairs to the sideline monitor, dons headphones, and ducks down like a cameraman in a Buster Keaton movie. While he does, both teams go out for extended lunches, Mayan ancestors reconstruct a pyramid stone by stone, and Halley's Comet comes around again. After consultation with the booth officials, the referee toggles a switch and reports: not enough evidence to overturn the call.

Boo. Boo! Booooooo! We was robbed. It ain't fair. Stone the ref. Call out the National Guard. Repeal prohibition. At the very least, confiscate Phil Simms's microphone. The hometown coach vigorously motions the ref over to the sidelines, jawbones, gesticulates, pleads incredulously toward the heavens. None of this changes the ref's mind. The home team loses a timeout.

Yes, it's irrelevant whether the back's foot nicked the sideline or not. What matters: whether enough evidence exists, from the officials' points of view, to overturn the original call. In these situations, one cannot think like a fan, an announcer, or an automaton. Above all coaches, highly competitive by training and aptitude, should not think like coaches. Better that they should think, and see, like replay officials.

All too easily, intense OCD coaches can transfer their competitive fervor from the game to the refs, as if the men-in-stripes had morphed into the opponent. Also, booth coaches, responsible for relaying replay results to the head guy, are prejudiced not just in favor of their own team, but in looking at film in a coach-centric way. We humans see through our eyes, not with them. Maybe NFL teams should hire filmmakers, with knowledge of how camera angles, lighting, framing, and other elements influence viewing, to assist in the booth.

Someday, NFL teams, as sample sizes increase, might keep stat sheets on replay officials, just as baseball hitters do on umpires' strike-zones, to determine different crews' tendencies in multiple circumstances. Even so, perfection will likely remain out of focus so long as human eyes do the looking.

A coach might ponder, also, before rotely throwing a challenge flag: does the possible gain from an overturned play outweigh the risk of squandering a timeout? For instance, if the above foot-out-of-bounds example, tweaked, meant the difference between a touchdown or a field goal attempt, and you trailed by four points in the fourth quarter, then you might want to dang well throw that challenge flag. However, in the example as given, does the difference between second-and-four and second-and-seven override the risk of losing a timeout?

Game situations do mitigate. For instance, a coach may want to call a timeout anyway, and a challenge may buy him extra seconds. Or maybe he wants to show an individual player that the head coach has his back. Perhaps he just wants to change the rhythm of the game. At any rate, head coaches already have enough to do during a game. They could benefit from reliable assistants up in the booth with immediate access to analytics regarding various scenarios.

Such game-management minutia may seem, well, minute. But in the hyper-competitive world of NFL championship football, every little detail matters. If you don't believe that, just ask 49er fans about last year's Super Bowl. The clock-management portion of game management did not by itself lose that game. Neither did it help to win it.