At the University of San Diego, the small Catholic school where Jim Harbaugh presumably threw his first sideline tantrum as a head coach, the stories they tell are about intensity and motivation. Then, as now, Harbaugh had both in large quantities.



On Feb. 3, he’ll be coaching the San Francisco 49ers in the Super Bowl. The fact he’s just seven years removed from coaching at USD, a non-scholarship program at the FCS level, would rate as a meteoric rise — except to those who know him.



“It really doesn’t surprise me,” said Jimmie Dougherty, an offensive assistant during Harbaugh’s three-year stay at USD from 2004-06. “He’s a great football mind. He gets the game first and foremost, but beyond that he’s a brilliant motivator. It’s been a fast rise, and it hasn’t been that long, but I think it’s cool that he’s never changed who he is or his approach to the game.”



The intense demeanor? The competitive nature? The will to win? Harbaugh had all of that, just like his father Jack and his older brother John, who will coach the Baltimore Ravens opposite Jim in the Super Bowl.



Ky Snyder, the USD athletic director who hired Jim Harbaugh, recalled a game at Princeton in 2005 when John, who was then special-teams coach for the Philadelphia Eagles, walked the sidelines carrying his younger brother’s headphones cord.



“In the fourth quarter, there were a couple of questionable calls, and it was a very close game that ended up being decided on the last play,” Snyder said. “Jim was out on the numbers arguing with the referees, and John is standing right behind him with the wires so Jim can get out there. The referee finally said, ‘Jim, this is your last warning. If you don’t get back on the sideline, I’m throwing the flag.’



“Jim said, ‘That’s a horrible call,’ and he turns around and starts moving back toward the sideline. But John stayed there and just fed Jim the wire back to the sideline and he finally said, ‘You guys are calling a bad game. You have to step up your game.’ The referee’s head turned around and he said, ‘Who are you?’ ”



Everyone knows the Harbaughs now. Theirs is a relationship built on love and competitiveness. Jim, a former NFL quarterback who spent 14 years in the league, had been the quality-control coach with the Oakland Raiders before he was hired at USD in 2004. He landed the job through his friendship with a priest who was a team chaplain for the San Diego Chargers, for whom Harbaugh played in 1999 and 2000 before retiring.



Between his playing days and that Raiders gig, he assisted his father at Western Kentucky, where Jack Harbaugh coached from 1994 to 2001. It was there he gave a glimpse of his coaching potential.



Snyder recalled hearing the story during lunch one day about when Jack worked for Jim as an offensive coach at USD.



“Jack ran the ball quite a bit at Western Kentucky,” he said. “One game, Jim grabbed the play sheet from his dad and said, ‘Do you have a passing play on this?’ He goes, ‘Here, call this,’ and he points to a play.



“So Jack calls the play. It’s a touchdown pass and they win the game. Jim throws the play card in the air and says, ‘See, it’s that simple.’ ”



Dougherty said Jim Harbaugh uses the same catch phrases now that he used during his tenure at USD. The first time he heard a 49ers player say, “Who’s got it better than us? Nobody,” he smiled.



“He was saying it back then,” Dougherty said. “There’s a lot of classic one-liners that he would say. That’s one of the coolest things that the former coaches on his staff at USD talk about.



“He’s a great motivator. He’s got great sayings, and obviously it’s working at the highest level now.”



Another Harbaugh favorite: “He always said that morale is to the physical as three is to one,” Dougherty said. “Basically, it means that morale is just as important as the physical in a football program. I always thought that was cool because it does go a long way on a team.”



None of his success surprises Snyder or Dougherty. They saw it coming. Seven years isn’t a long time, but Harbaugh’s rise from USD to Stanford to the 49ers was an especially fast track, one that is taking him to the Super Bowl in three seasons.



“It goes quickly,” Snyder said. “One thing I’ve learned is that you never underestimate Jim Harbaugh. Don’t even put a time frame on how long it will take him to get something done. If you say he can’t, he’ll figure out a way he can.”