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49ers’ Harbaugh facing greatest challenge

Jim Harbaugh is going to really have to work his magic this season. Every speckle of miracle dust. Every drop of his secret potion.

Sunday’s come-from-ahead loss to the Chicago Bears is the latest adversity Harbaugh must lead the 49ers through. Even worse, it might be the sign it’s all too much to overcome.

Everyone figured Seattle would be the biggest challenge for the 49ers. But before any attention can be paid to the Seahawks, the 49ers need to address their own problems, which are aplenty. On-the-field issues and off-the-field drama are piling up to make for an especially daunting Super Bowl run.

This the biggest test of Harbaugh’s NFL coaching career, trying to get the 49ers to navigate it all and meet expectations of being a top team.

If he pulls this off, he will have vindicated his presumed stance that he deserves to be the among the league’s highest-paid coaches. A successful finish this season might be enough to warrant more power, if he wants it, elsewhere.

The football-related struggles alone are enough to derail expectations. The 49ers lost All-Pro linebacker NaVorro Bowman, zapping some elite talent from that defense. Another star, Aldon Smith, has seven more games to serve on his suspension. Starting nose tackle Glenn Dorsey is sidelined at least until midseason. The starting secondary has three new members trying to work as a cohesive unit, and one of those three, cornerback Tramaine Brock, is out with a toe injury.

And that’s just one side of the ball.

On offense, the 49ers are down to two running backs, Frank Gore and Carlos Hyde, which is plenty good until one of them gets banged up. The offensive line is suffering from an injury to tackle Anthony Davis, and center Daniel Kilgore has only two games under his belt as an NFL starter.

And then, to top it off, Colin Kaepernick was a straight-up mess on national television Sunday night.

With the star quarterback proving his doubters right for a night, the 49ers looked closer to mediocrity than to a sixth Super Bowl.

“Nobody feels real good about it,” Harbaugh said about the Bears game at his weekly news conference Monday. “It’s a bad feeling to lose a game, no matter how you lose it, what circumstances there were. Being ahead in the game and not finishing the game with a win leads to very bad feeling after the game.”

But these football issues must be resolved at the same time that an anvil hangs over the franchise.

A turbulent offseason — legal issues with Smith and cornerback Chris Culliver, right guard Alex Boone’s contract holdout — went to another level with defensive tackle Ray McDonald’s Aug. 31 arrest on suspicion of felony domestic violence.

The 49ers now have a significant role in the NFL’s edition of “Law & Order” — an unsavory show that stars the Baltimore Ravens (Ray Rice), the Carolina Panthers (Greg Hardy) and the Minnesota Vikings (Adrian Peterson). The 49ers aren’t a leading character, at least not yet, but their decision to keep McDonald in uniform has made them part of a national story about how the NFL deals with players who have been arrested.

And Harbaugh, more than anyone else in the organization — right or wrong, for better or for worse — is at the forefront of defending the 49ers’ position on the matter.

In addition to taking the questions, and absorbing the blows, from those who disagree with the team’s stance on McDonald, he also needs to coach the team. Double-duty wasn’t so difficult last week, coming off an impressive performance in the season opener at Dallas. But this week, Harbaugh must rally a team that lost, that beat itself, that blew a 17-0 lead amid a hellstorm of penalties and turnovers and now must go on the road to play a 2-0 Arizona team.

Oh, and the 49ers might be missing another star, tight end Vernon Davis, who was injured in the second half Sunday.

But this is where Harbaugh excels — turning adversity into advantage, using obstacles as the gate to close ranks. There was some of that in the season-opening win at Dallas. The 49ers came out on fire, as one, and roared to a 28-3 lead.

The perfect rebuttal to the doubters, to those who questioned the franchise’s character and resolve.

If the 49ers ever needed the best of Harbaugh, it’s right now. If a fourth consecutive NFC Championship game is to be reached, it will be because Harbaugh performed at his peak.

“I’ll make a boxing analogy,” Harbaugh said. “You’ve got to get off the canvas. We’re in the business of winning your next game and doing everything possible that you can to make sure that doesn’t happen again. That’s the mindset.”

Harbaugh