The San Francisco 49ers restructured the contracts of Vernon Davis, Carlos Rogers and Ray McDonald in order to fit NaVorro Bowman's $7.5 million signing bonus under the cap, according to a source.

Bowman, whose original four-year deal averaged $623,062 annually through 2013, signed a five-year extension this week through 2018 that averages $8.911 million annually.

Because of his signing bonus, Bowman's 2012 cap figure immediately rose from $717,887 to $2.217 million, the source said.

Davis provided the biggest cap relief for the 49ers. Davis' 2012 cap figure went from a little over $8 million to $6.8 million. The 49ers awarded Davis a $1.48 million signing bonus and had his remaining $25,000 per game active roster bonuses for the final five regular season games designated as an OATSB item (other amount treated as signing bonus).

Jim Harbaugh has placed Alex Smith in a difficult position, making him the San Francisco 49ers' backup quarterback upon return from a concussion.

Harabaugh's former NFL teammates don't believe he would have handled it as gracefully as Alex Smith.

"..The Jim Harbaugh who I knew, who was feisty and competitive, he wouldn't have handled it well," said Ray Buchanan. "I don't think he'd have handled it as well as Alex did. He'd have been a lot more outspoken with the coach. He would cause a little more havoc. And he probably would have spoken out to the media as well."

"The Jim Harbaugh I knew would be going crazy," Tony Siragusa said. "He would not stand for that. He would be going ballistic. But Jim Harbaugh the player and Jim Harbaugh the coach are like two completely different people."

Alex Smith spoke publicly for the first time since Jim Harbaugh named Colin Kaepernick the starting quarterback of the San Francisco 49ers this week against the Rams.

“It sucks,” said Smith. “I don’t know what else to say.”

Smith suffered a concussion several weeks ago and Kaepernick has played well in his absence.

“No resentment,” Smith said. “I don’t get to make those decisions. That’s what he gets paid to do. He’s the head coach. I play football. That’s what I’m going to continue to do. Continue to get ready. And make the most of my next opportunity.”

The San Francisco 49ers will start Colin Kaepernick at quarterback on Sunday against the Rams.

Kaepernick assumed the starting role following a concussion by Alex Smith.

The San Francisco 49ers auditioned Billy Cundiff and Nate Kaeding on Tuesday.

David Akers has struggled with his consistency this season.

Kaeding is the most-accurate kicker in NFL history.

NaVorro Bowman and the San Francisco 49ers have agreed upon a new contract.

Bowman's deal is worth as much $45.25 million with $25.5 million guaranteed.

Bowman and Patrick Willis comprise the best inside linebacker tandem in the NFL.

"NaVorro epitomizes what we look for in a 49er," 49ers general manager Trent Baalke said in a statement. "We are excited that the All Pro tandem of Willis and Bowman will be together in red and gold for years to come."

Kendall Hunter will miss the remainder of the 2012 season with a left Achilles tear.

Hunter had 371 yards and two touchdowns on 72 carries for the San Francisco 49ers this season.

LaMichael James and Brandon Jacobs will assume backup running back duties behind Frank Gore.

Kyle Williams will miss the remainder of the 2012 season with a torn ACL.

Williams handles kick return duties for the San Francisco 49ers.

“Regret to inform y’all I will be out for the season with a torn ACL,’’ wrote Williams on his Twitter account. “Not how I saw things playing out, but in the end I will be fine.

“This is just another obstacle. I will have to climb back.”

Colin Kaepernick has been receiving the unwavering support of Alex Smith in what is a difficult situation for both quarterbacks of the San Francisco 49ers.

Kaepernick went 16-for-25 for 231 yards, one touchdown and one interception, while rushing for 27 yards and another touchdown.

"It's got to be tough,'' said Kaepernick, "but Alex is so good to me. Our relationship is still the same as it's been. Every time I came off the field, he'd say to me, 'Did you see this?' Or, 'Did you see that?' Alex is a great guy.''

Jim Harbaugh isn't committing to Colin Kaepernick or Alex Smith as the starting quarterback of the San Francisco 49ers.

But Vernon Davis still believes in Smith.

"It's difficult, but I think Alex is still the man," Davis told reporters following the 49ers' win over the Saints on Sunday. "In my heart I strongly believe that and you'll know next week. I'm sure Harbaugh will make a nice decision who he wants to go with but right now we have two outstanding playmakers.

"I'm sure Alex is still our guy," said Davis.

Davis had just one target by Kaepernick in Sunday's game and zero catches.

"I think I should (be the starting quarterback) but it's not my decision," Smith said after Sunday's win. "Also, I'm part of this team and it was great to go out and get a win."