Alex Smith has had his ups and downs in his career and with the 49ers staying in the hunt for a playoff spot he has an opportunity to make the best of a rare second chance.  Smith finished his rookie season in 2005 starting the last nine games of the season with one touchdown and 11 interceptions.  Norv Turner was hired as offensive coordinator in 2006 and Smith slightly improved throwing 16 touchdowns with 16 interceptions.  He became the first Niner QB to take every snap under center in a season.  The Chargers hired away Turner the following season and replaced by quarterback coach Jim Hostler.  Hostler had no prior play calling experience and Smith’s progress stalled.  It marked the beginning of a downward fall for Smith as he separated his right shoulder in week 4 of 2007.  He would miss the next three weeks and come back for three games in which he was ineffective only to sit out the rest of the season on injured reserve because of his shoulder.  During this period Mike Nolan questioned Smith’s toughness by saying his shoulder injury was not as bad as being perceived.  The criticism took a toll on Smith’s confidence.  In 2008 he competed for the starting job but lost it to J.T. O’Sullivan and then before the start of the season he broke his right shoulder blade.  I labeled Smith a bust at that point as he would be sitting out the whole season and lost the starting job even if he was healthy.

Smith looked like he was not going to get a second chance to be a starter not only with the 49ers but with any other NFL team but he restructured his contract this off-season and took a significant pay cut to remain with the 49ers.  We know how the story goes up until now and Smith is ready to put himself back into the starting quarterback role for good this time but only if he can lead the 49ers back to the playoffs.  It will be an uphill battle for Smith and the 49ers because they will probably need a 4-1 record down the stretch to clinch a playoff spot.  Either way Smith will be counted on to lead the 49ers to wins as the offensive playbook has been adapted to his skills and abilities.  This time he has no excuses because of the spread formation and the talented receivers around him.  This is his chance to make a name for himself and disprove the bust label because a third chance will likely not come.

Offensive lineman Barry Sims was interested into the game after the first play and held his own against the defensive end Dwight Freeney.  But to lose a player like Staley for six weeks this late into the season will stall the 49ers offensive progress as the rest of the offensive line has had suspect play.  The 49ers are in a tight spot as the only other tackle available on the team is Chris Patrick who has spent almost all of his career on the practice squad on six different teams since he was signed in 2007 as an undrafted rookie free-agent by the New York Giants.  This is not good for the 49ers offensive line.  Someone needs to set-up their play on the line if they 49ers want to continue progressing their offense while Staley is out.

The replacement for Clements will be Brown who started in his place against the Colts.  It is not known if Clements had not injured himself would he have started again at cornerback.  Mike Singletary only said that Brown was named the starter because he matched up better against Colts wide receiver Pierre Garcon.  We may never know if Clements really lost his job for one game or for the rest of the season but we may have an idea at the end of the season as he will make at least $6 million in salary next year.  GM Scot McCloughan will most likely ask Clements to take a pay-cut or be released with his bad play not only this year but last season.  While Clements has had some good games as a Niner he has not been the shut down corner the 49er Faithful thought we were getting when he was with the Bills.

The 49ers suffered injuries to the two weakest parts on offense, the line, and on defense, the secondary.  Brown will be a good replacement for Clements as he almost wrestled the starting job from other cornerback Shawntae Spencer in training camp.  I hope that Sims can build on what he did last week against the Colts and provides the same protection that Staley did so successfully.

• Crabtree and his agent Eugene Parker were holding out for the guaranteed money that the first wide receiver picked in the draft, Darrius Heyward-Bey at number seven, received which was $23.5 million.  Crabtree’s contract is $17 million of guaranteed money, which is only a million higher than the $16 million the 49ers first offered Crabtree.  Advantage McCloghan.

• The contract Crabtree signed was a six-year deal worth $32 million that can turn into a five-year deal if he meets incentives.  The sixth year would be voided if he goes to the Pro Bowl during his first four years, along with playing 80 percent of the offensive snaps during a separate season in which the 49ers reach the playoffs.  The deal can be worth up to $40 million if he achieves every incentive in the deal.  I want Crabtree to reach these incentives but with receivers like Larry Fitzgerald, Steve Smith, Anquan Boldin, Calvin Johnson and Roddy White in the NFC going to the Pro Bowl might be hard for him to achieve.  He has lost one year, this year, so let’s see how he does the next three years.  Advantage McCloughan.

• A positive for McCloughan and even team president Jed York was the fact that they never said anything negative about Crabtree publicly to try to pressure him into signing.  We have seen owners do this in the past and it has worked but the 49ers organization knows it has a good team with or without Crabtree and publicly pressuring the former Texas Tech star would be a bigger distraction for the team.  Advantage McCloughan.

• Who gave in? Crabtree of course.  McClouhan at no point gave into the demands of Crabtree and his inner circle.  He said the offer is what is, take it or leave it.  He did not receive the money he was looking for and the 49ers gave him more money in guarantees than originally offered but it was lower than the 9th pick B.J. Raji’s $18 million and higher than the 11th pick, Aaron Maybin, received which was $15 million.  The more money guaranteed is also because it is a six-year deal rather than a five-year deal.  Advantage McCloughan.

No one will really know why Crabtree decided to sign.  Was it the 3-1 start by the Niners?  Was it the Jets trading for WR Braylon Edwards and him thinking that he would not get the money Deion Sanders was saying two other teams would pay him?  Was it selfishness, like the holdout, that made him sign?  Meaning he knew how much money he would lose by sitting out the season and also hurting his draft stock value if he returned to the NFL draft next year.

I think the real question is, what were Crabtree and his inner circle thinking at the start of the holdout?  I think they saw weakness in the 49ers organization that they would cave to their demands and offer a contract Crabtree was holding out for.  Some examples are former number one pick Alex Smith and the guaranteed money that they over paid him and the huge contracts they gave free agents Nate Clements and Justin Smith which were also way overvalued.  Eugene Parker thought he was a good agent and told his client to holdout.  Crabtree thought he was a better player than Hayward-Bey and believed in his agent by holding out.  I think Crabtree and Parker had the fourth week of the season as their line drawn in the sand for them to sign.  Thing is, they thought the 49ers would give in before then.  Instead it was them and now both look silly as the 49ers Faithful and the rest of the NFL wonder, why the long holdout for a contract that was the same as the one initially offered?

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