Jim Harbaugh Colin Kaepernick 49ers week 1Jim Harbaugh probably doesn’t have many complaints about his current starting quarterback. It seems like every one he’s had the chance to work with over his coaching career has thrived under his guidance, from Josh Johnson at University of San Diego and Alex Smith in 2011 to Colin Kaepernick, last year and now.

But if you injected Harbaugh with truth serum, he might just tell you his most special pupil was Andrew Luck.

With the Colts coming to Candlestick Park on Sunday, Harbaugh described this game as “quite a bit of a reunion.”

“That’s not a good thing … Because they’re good.”

Connections between Harbaugh’s 49ers and Luck’s Colts are ample. Pep Hamilton — an assistant coach under Harbaugh who took over as offensive coordinator once David Shaw became head coach — is now the offensive coordinator in Indianapolis. The Colts took Luck’s favorite target, tight end Coby Fleener in the second round of the 2012 draft. They also added Griff Whalen as an undrafted free agent. There’s even the added storyline of Ricky Jean-Francois coming back to face the team that drafted him and helped him become a coveted free agent.

But of all the connections, nothing seems to linger more than Harbaugh’s relationship with Luck. It was evident in the way the coach described his old quarterback.

“He is a, for lack of a better term, a freakishly good athlete,” Harbaugh said. “He’s a lot faster than you think he is, and he’s really fast. Stronger than he looks, but then you see the evidence on tape. Where guys are hitting pretty solid, pretty hard and he’s able to just flinch it off, kind of Roethlisberger-like. Throws with a lot of velocity even though it’s a throwing motion that’s pretty smooth. Ball comes out a lot faster than you think it does, and with a lot more velocity than you think. Just very, very blessed athletically.”

I asked Harbaugh how teams can confuse Luck on the football field, but he was as baffled as I was.

“That’s an interesting question and a good one,” he responded. “The answer isn’t a real good one because there’s not a lot that confuses him or rattles him or that he doesn’t handle well. He’s just that kind of player.”

Harbaugh compared Luck to Roethlisberger yet again when asked about his toughness and his ability to extend plays.

“When you get hit hard he’ll pop back up and pat somebody on the shoulder or helmet and say, ‘nice hit.’ He’s got the ability to extend plays. I saw the game-winning touchdown against Oakland in the opener. Over and over, examples of his ability plays with his feet and also with his strength. Very much like Roethlisberger does.”

While it’s clear he has an equally talented (albeit different) quarterback in Kaepernick, the evidence of a relationship gone is still there. Nevertheless, Harbaugh found a way to wrangle to conversation back and praise Kaepernick when discussing first impressions. He said meeting Luck “was similar to Colin with their enthusiasm.”

“How they interact with their teammates and coaches, really everybody that they come in contact with. Real gentlemen, both of these two young men.”

Extra Points

— Kaepernick might have let some frustration slip when he was asked about Seattle’s secondary:

“I think they get away with a lot of things on defense, but I think the biggest thing is we have to go out and execute,” Kaepernick said. “It’s not really something they did, it’s what we didn’t do.”

— Harbaugh said newly acquired fullback Owen Marecic will be a backup to Bruce Miller and play a role on special teams. He denied Marecic’s potential as a two-way player like he was at Stanford.

— The coach also said they “feel confident with Tony Jerod-Eddie” as a backup nose tackle, now that Glenn Dorsey has been thrust into the role of a starter.

— Eric Reid was at practice sporting a blue non-contact jersey, but Justin Smith, Ray McDonald and Vernon Davis were all in the weight room out of pads. Aldon Smith had his left knee wrapped up and didn’t participate in individual drills.

— Harbaugh said there were “no setbacks” in Reid’s recovering from his concussion.

“He felt good, felt clearn without any symptoms,” Harbaugh said, “and that’s remained the case.”

— LaMichael James was on the side field (as I like to call “Lattimore Land”) doing stretching and rehabilitation drills in sweats. Michael Crabtree was doing some rehab work there as well.