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Jim Harbaugh, 49er Head Coach runs drills during organized team activities also known as spring practice at the 49ers training facility in Santa Clara, Calif. on Wednesday, May 23, 2012. Players are Rock Cartwright (28) and Colin Kaepernick (7). (Gary Reyes/ Staff)

Some 21/2 months after Peyton Manning worked out for the 49ers in North Carolina, coach Jim Harbaugh came forward Wednesday and clarified the 49ers' interest in the four-time NFL MVP, who eventually signed with the Denver Broncos.

Harbaugh concluded his post-practice media session Wednesday with the following dialogue:

"Oh one other thing: There's a perception out there, and it's an erroneous perception, that we were flirting with Peyton Manning.

"I keep hearing it over and over. It's silly and it's untrue. It's phony. Even the perception that we were pursuing. We were evaluating."

The topic resurfaced in the past few days when Carolina Panthers linebacker Jon Beason responded to Alex Smith's comments how Cam Newton's 300-yard passing games didn't translate into Panthers victories.

Beason, on Twitter, wrote: "Alex smith, don't hate on Cam Bc your stats would've gotten u cut if Peyton decided to come 2 San Fran.Truth b told. That's after a 13-3 yr."

Harbaugh continued Wednesday: "I've said all along that Alex Smith has been our quarterback. There's no scenario, other than Alex choosing to sign with another team, that we would consider him not as our quarterback.

"We don't like to compare or talk about someone on another team. But in this case, it's time to set the record straight.

"Alex Smith is our quarterback. Was our quarterback. Had every intention of always bringing him back. There would have been no circumstance that would have let Alex Smith go.


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"Were we out there seeing and evaluating if we could have them both? Heck yeah. We evaluate and eliminate the possibility.

"For further evidence, we would not have given any player out there in free agency a sixth of our salary cap, and let six or seven of our own guys go."

On March 19, Manning committed to the Broncos and received a five-year, $96 million deal. He played 14 years with the Indianapolis Colts before multiple neck surgeries sidelined him for the 2011 season.

One day after Manning called Harbaugh to personally relay his intentions, Smith came to terms with the 49ers on a three-year, $24 million deal that makes his 2012 salary-cap figure $9.25 million, according to CSN Bay Area.

So did Manning call the 49ers and express interest in joining them?

"Yeah there was interest," Harbaugh responded. "We evaluated it and pursued it. Er, evaluated it, and there were conversations. I'm not going to go into all the personal conversations.

"There was nothing said to Alex that was not said to Peyton Manning or in-house here, on the record, off the record. Both those young men knew exactly what our intentions were. It was very clear about that: That Alex Smith would be back as our quarterback in 2012 if we could make that signing."

Smith backed up Harbaugh's contention in an interview later Wednesday.

"They've been up front from the beginning, constantly in talks with me and negotiating with me and that was never off the table," Smith said. "It was simply a fact that, ya know, potentially gonna have to compete with somebody and he'd earned the right to compete for the job and this was my job to compete for."

On March 18, Smith paid his one and only free-agency visit to the Miami Dolphins. Meanwhile, Manning was believed to be debating among three finalists: the Broncos, 49ers and Tennessee Titans.

Manning, who shares the same agent as Smith, has never indicated whether he thought he would be competing with Smith if he joined the 49ers.

Upon picking the Broncos, Manning told the Denver Post he enjoyed getting to know Harbaugh. As for pursuing another quarterback's job, Manning said: "I'm in the quarterback fraternity, and it's a unique fraternity. I've hated that about all of this, whether it was (the Titans') Matt Hasselbeck or Alex Smith, you know, I just didn't know how else to do it."

A day after losing in the NFC Championship game, Harbaugh reiterated his preference for Smith to return but added "that's never an anointed position." A month later at the NFL scouting combine, Harbaugh termed Smith "our guy."

What did Harbaugh think of Manning after that March 13 workout at Duke University, a workout that was kept secret until ESPN reported it three days later?

"Well, we thought that was a critical thing to do," Harbaugh said of working out Manning. "He's coming off a season where he was injured and didn't play. He's going to be a fine player in the National Football League. He made the best decision for himself going to the Denver Broncos. Wish him nothing but success. He'll be fine."

The 49ers and Broncos will meet Aug. 26 in Denver in each team's third exhibition game.

If the 49ers did sign Manning, would they have had to severely adjust their roster to fit him under the salary cap?

Said Harbaugh: "We're not going into all that. It's not your right or anybody's right to go into that. But you could understand. The best fit for us was Alex Smith. We weren't going to give a sixth of our salary cap to anybody."

If Manning said yes to the 49ers, would Smith have been here as well?

"That would have been the hope, yeah," Harbaugh responded. "You don't control all those factors."

When Smith officially re-signed with the 49ers, he said he would have "relished the opportunity" to compete with Manning for the 49ers' job. On Wednesday, in the wake of Harbaugh's comments, Smith offered the same stance.

"I certainly felt like this was my job to compete for. Without question," Smith said.

Smith, in his seventh season, started every game while the 49ers went 13-3, won the NFC West and reached the NFC Championship game.

Regarding his visit to the Dolphins, Smith said he merely was playing "the business side" of free agency. "For me though, this was always the place," he said of the 49ers.

By speaking up Wednesday, Harbaugh hoped to talk about any alleged pursuit of Manning.

"Hopefully that sets the record straight," Harbaugh said. "I don't want you to keep reporting the silliness and phoniness."

For more on the 49ers, see Cam Inman's Hot Read blog at blogs.mercurynews.com/49ers.