The Cubs never even watched Kaepernick throw a baseball before drafting him in the 43rd round almost four years ago. They did watch him throw a football for Nevada, and decided that college game told them more than enough.

Ultimately, the Cubs just couldn’t lure Kaepernick away from his first love: football. Now, he’s headed to the Super Bowl to lead the San Francisco 49ers against Baltimore on Feb. 3.

Hughes, the longtime national cross-checker in the Cubs’ scouting department, and several others, including then-general manager Jim Hendry, figured they should give it a shot and hope Kaepernick might reconsider.

“Yeah, that wasn’t happening,” Kaepernick said with a smile Wednesday, shaking his head.

Hughes tried for two weeks to convince Kaepernick, who had made it all but clear he wouldn’t sign. He was surprised anybody drafted him at all given he had been so upfront about sticking with football.

But Chicago’s NFL sources — Hughes said three different teams — figured Kaepernick would be a late-round pick or even someone who might have to go the route of the Canadian Football League.

That seems so laughable now. The Niners picked Kaepernick in the second round of the 2011 draft, made him the starter midseason this year and now will ask him to carry them all the way to the franchise’s sixth championship in what will be just his 10th career NFL start.

“I was looking at this tall, kind of gangly at the time quarterback that was super athletic and had this really long throwing motion,” Hughes said. “I was talking to some of my buddies at Reno and said, ‘Boy, I wonder if this kid’s ever played baseball, he’s got an arm stroke like a pitcher.’”

That sent Hughes on a fun little research project. Kaepernick regularly threw 90 mph in high school, but was now some 40 pounds heavier as a college football player.

He certainly would throw harder.

“So, I was definitely intrigued, bigger, stronger, more athletic,” Hughes said. “Colin had no idea we were even considering drafting him. I kind of caught him off guard when I called him after we drafted him. He kind of got a kick out of it and said his phone was ringing off the hook that he’d been drafted by the Cubs. He had no idea.”

Then-Nevada coach Chris Ault had the challenge of developing Kaepernick’s football motion — and that wasn’t an easy task with the QB having been a pitcher.

“His first two years he was a thrower from his pitching days. It was all sidearm,” Ault said. “That was a habit we had to break. You could see his throwing motion, timing and touch was there. His senior year I saw the whole package. He was a guy ready for the NFL who could do all things they’d like him to do plus run. Now I look at him with the Niners and Jim and those guys are doing a super job. He has all the throws. What I really enjoy watching is he really learned to put the touch on the ball when he has to.”

49ers coach Jim Harbaugh can appreciate the Cubs’ attempt to recruit Kaepernick to baseball. He would have tried, too, had he been in their position.

“He’s a man for all seasons,” Harbaugh said. “Tremendous football player, basketball player, baseball player, a tremendous athlete with a lot of gifts of God. And a tremendous competitive fire, readiness and willingness to compete, to be able to make cool-headed decisions under fire. Who wouldn’t want a player like that in baseball or football?”

Or basketball, for that matter.

Kaepernick was a three-sport star at John H. Pitman High in Turlock, a couple of hours east in California’s Central Valley.

At 6-foot-4 and about 180 pounds as a high school senior, he went 11-2 with a 1.27 ERA with two no-hitters and 10 complete games — now-retired Pitman coach Mick Tate couldn’t remember Wednesday if there was a second, but the quarterback sure knew.

“There were two,” Kaepernick said.

Kaepernick batted .313 with 17 RBIs and a .407 on-base percentage. In basketball, he averaged 15.4 points.

“The thing we’re most proud of, those who coached him in high school, is we want to make them better people,” Tate said. “We didn’t have to work very hard to make him a better person.”

And those close to Kaepernick had a pretty good idea which way he was headed.

“He was a phenomenal basketball player here,” said Philip Sanchez, Kaepernick’s high school guidance counselor who remains a close family friend. “Don’t forget that. People think of it as just baseball-football, no. He went from football, the very next day he was leading his team in basketball. Then the very next day when basketball ended, now it was time to start pitching. That’s rare that you get kids who play three sports these days.”

The Cubs figured they had reason to be somewhat optimistic of swaying Kaepernick. They have had success drafting football players, such as pitcher Jeff Samardzija and outfielder Matt Szczur — a pair of former star college wide receivers who picked baseball.

And Kaepernick had tremendous “upside,” a common phrase the scouts use to describe potential.

The 49ers saw the same upside. Harbaugh made a midseason switch to him as starter over Alex Smith, the 2005 No. 1 overall draft pick.

“We’re not really surprised at his success, because he’s always had success,” Sanchez said. “I’m just happy that the world has seen the person that we know.”

At Pitman, they sure appreciate Kaepernick to this day.

So do the folks in Reno.

During the San Diego State-Nevada basketball game Wednesday night, the plan was for everybody to pose Kaepernick style, flexing the right biceps muscle and kissing it — a new sensation known as “Kaepernicking.”

Even the Cubs folks are cheering for him.

“I’ve followed him since the first time I saw him. He’s a very entertaining, fun guy to watch, great athlete, great competitor, very good arm strength, good touch, good feel,” Hughes said. “After I drafted him, I talked to him and his father, Rick, four or five times each throughout a two-week period trying to convince him to give baseball a shot. I got to know him through several conversations and since then I’ve shot him a few text messages — in college after they beat Boise State, which was huge, and after he got drafted by the Niners. A credit to him, I talked to him over a two-week stretch and he didn’t know me from Adam and he has returned each one of my text messages. That says a lot about the young man.”