Before the game, Jim Harbaugh got all shoulder-slappy intense with Colin Kaepernick, who had trouble keeping a straight face.

After the San Francisco 49ers lost 16-13 in overtime to the St. Louis Rams, Harbaugh gave a vote of confidence of sorts to his second-year quarterback.

“I’ll let you know if there’s a change, but right now feel as if it’ll be the same as this week,” said Harbaugh, who earlier this week announced that Kaepernick would start in St. Louis because he had “the hot hand.”

Presumed stability at the quarterback position shouldn’t be a surprise, even though Kaepernick made two huge mistakes in a loss where the 49ers’ defense played more than well enough to win. How can Harbaugh back away from Kaepernick now, after he and Greg Roman were so clearly out-schemed?

After two games against the 49ers, Jeff Fisher definitely has the hot hand if we’re comparing coaches — and not just because he has a better placekicker at his disposal. Except for one wild play (a 50-yard run for Kaepernick in the fourth quarter), Fisher’s defense confused Kaepernick, pressuring him without letting him escape for big gains on the ground.

The 49ers’ offensive line has certainly played better, but it appeared as if the Rams knew what the 49ers were doing on nearly every play. Strangely, the 49ers were conservative and aggressive at the wrong times. If Delanie Walker catches that potential touchdown pass with a couple minutes to go, nobody says anything. Then again, Walker has dropped passes all season and running at that stage in the game would have drained the clock and forced the Rams to take timeouts. In overtime, the 49ers weren’t exactly content to let David Akers attempt a field goal from 50+. However, two vanilla Frank Gore runs, followed by a play where Kaepernick rolled to his left (and threw it away), didn’t help San Francisco’s cause.

The 49ers brought in two kickers for tryouts this week, so they know Akers isn’t dependable from long range. He hasn’t kicked a 40-yarder in a month and hasn’t made a field goal of 50 or more yards since Week 1. But the key isn’t finding a kicker who’s a lock to make a 51-yarder in overtime — the few kickers who can be counted on to do that are already employed (just check out Nate Kaeding’s postseason record if you wonder how he’d do under pressure). No, the coaches need to make sure that when they’re gifted with extraordinarily good field position in sudden death overtime, they put their team in a position to finish the game without having to count on Akers suddenly finding his stroke.

The 49ers were also flagged nine times for 82 yards, and penalties are generally considered a coaching problem as well. It’s going to be a long plane ride home for Harbaugh and his staff.

Calling out Kap

One could also find fault with the coaching staff for calling a read option play near their own goal-line, but that’s the reason why Kaepernick is now the starter — he allows the coaches to maintain an air of unpredictability. It’s up to Kaepernick not to cause turnovers, especially while holding an 8-point lead on that area of the field.

Kaepernick’s favorite quarterback as a youngster was Brett Favre, who threw a lot of shovel passes. The main difference was Favre almost always shoveled forward. Kaepernick flung the ball toward the goal-line with the type of recklessness that Alex Smith’s supporters have warned us about for the last few weeks. Some are blaming Ted Ginn for allowing Janoris Jenkins (who can’t cover the slant to save his life, but has now scored three touchdowns in the last two games) to pick up the ball, but Kaepernick shouldn’t have put him in that position. Ginn was probably in shock that Kaepernick tossed the ball like that, as we all were.

The safety was also caused by an egregious mental error occurring when Kaepernick was running with the ball. Mike Pereira thought it might not have been intentional grounding (the line of scrimmage extends out of bounds during those plays, and it appeared that Kaepernick’s pass went far enough) but what was Kaepernick doing in the end zone on a play that started at the 49ers’ 17-yard line?

On the subject of end zones, Kaepernick has led the 49ers to just three touchdowns in the last two games. He has shown flashes, but his play has never quite measured up to that fantastic first half against Chicago — 30 glorious, action-packed minutes that led to him becoming an NFL starter. In that half, Kaepernick stretched the field with his arm and Vernon Davis looked like a new man. Except for passes of 22 and 30 yards to Michael Crabtree, there were no passes of longer than 20 yards and very few shots taken downfield. When the running game is bottled up and the 49ers’ passing attack looks like San Francisco’s offense on Smith’s worst day, points are hard to come by on the road.

After averaging an insane 9.2 yards per attempt going into today’s game, the Rams held Kaepernick to a pedestrian 6.5 yards per attempt. In case you’re wondering, Miami (next week’s opponent) came into Week 12 allowing 7.1 yards per attempt to opposing quarterbacks … the same figure as the St. Louis Rams.

Missing Kendall Hunter

How bad must LaMichael James look in practice? After Hunter tore his achilles it seemed like James would finally get his shot after 10 straight times on the inactive list. Instead, it was A.J. Jenkins who was activated for the first time since Week 1 while James watched another game in street clothes. Gore carried the ball a season-high 23 times with minimal success (58 yards total; only 21 yards on the 17 carries after his first quarter TD) and Brandon Jacobs was even worse in his three rushing attempts, gaining only 5 yards (although he did convert one third down).

It looks like we’re on a collision course with Jenkins playing a role in games, as Mario Manningham left the game with a shoulder injury. If he misses time, Jenkins becomes the No. 4 WR behind Crabtree, Randy Moss and Ted Ginn.

What about Alex?

After Greg Zuerlein launched the 54-yard field goal to win the game as if his right leg was an actual cannon, Fox quickly showed the closeups you’d expect. Here’s how Kaepernick looked:

And it sure looked like Alex Smith had the “Yeah, playing QB in the NFL ain’t that easy, is it” smirk going…