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Ben Margot / The Associated Press

Colt McCoy, the 49ers' No. 2 quarterback, appears to be the reason the team keeps searching for a veteran backup.

Matthew Barrows: Is Harbaugh uneasy with McCoy?

Published: Friday, Oct. 4, 2013 - 12:00 am | Page 1C
Last Modified: Saturday, Oct. 5, 2013 - 2:59 pm

SANTA CLARA – Jim Harbaugh is the quarterback whisperer, the man who discovered Josh Johnson, who built Andrew Luck and who resurrected Alex Smith. His instincts regarding all things quarterback have been spot-on since he became a head coach.

By all accounts, the decision to sign John Skelton and expose rookie B.J. Daniels to the waiver wire this week was Harbaugh's. And since he's built up so much quarterback credit, we have to assume he's doing the right thing for the 49ers.

But we don't have to buy his explanation.

Harbaugh said Skelton was added to the mix because the 49ers needed a veteran backup with NFL starting experience, which Daniels, a seventh-round draft pick, did not have.

The 49ers, however, already had veteran backup Colt McCoy.

Most teams with three quarterbacks have a starter, a backup and a young player they try to develop. The 49ers had that in Colin Kaepernick, McCoy and Daniels, but Harbaugh wasn't content with the arrangement.

Harbaugh's issue wasn't with Daniels, the quarterback he jettisoned, but with McCoy, the guy who remains – for now – in the No. 2 spot.

The late-August quarterback competition between McCoy and Scott Tolzien, the sudden signing of Seneca Wallace late in the preseason, the restructuring of McCoy's contract and now this, the addition of Skelton, all point to one thing – Harbaugh is uneasy with McCoy running the team if something happens to Kaepernick.

Harbaugh and the 49ers wanted to add Daniels to the practice squad before the Seahawks snatched him away Wednesday. And they would have given him his full, active-roster pay.

The plan appears to have been to allow Skelton to learn the offense, and once he did, have him compete for the No. 2 job. After that, either McCoy or Skelton would have been cut and Daniels added back to the 53-man roster.

Skelton's trip to Tennessee on Tuesday also may have prompted the 49ers to make a move sooner than they preferred.

"I had a workout with the Titans," Skelton said Wednesday. "And I think as soon as people (in Santa Clara) caught wind of that, they flew me back out."

If the 49ers had signed Skelton later in the season – perhaps just before the bye week – it would have given him more time to get comfortable with the offense. Under that scenario, they may have released McCoy, not Daniels.

Whether Harbaugh's move was shrewd or foolish will depend on Daniels' development.

During the preseason, Daniels seemed to be another one of Harbaugh's quarterback finds, someone with natural leadership skills who had the athleticism to run a multi-threat offense similar to the way Kaepernick operates.

He also fit the 49ers' strategy, which is to develop young passers and then parlay them into extra draft picks the way the Eagles and Packers used to do.

That's still the plan. The draft is expected to have plenty of quality quarterbacks, and the 49ers have an abundance of draft picks they can use to select the one they want.

But it was the Seahawks – the 49ers' archnemesis – who grabbed Daniels, adding more intrigue to the decisions.

Daniels will learn from Russell Wilson, one of the NFL's best young quarterbacks who has much in common with Daniels. Both are 5-foot-11 and they have similar skills.

The intensity of the 49ers-Seahawks rivalry means the decision to let Daniels go won't fade away like most ordinary early October transactions. If Daniels sticks with Seattle, every Seahawks-49ers game will be a reminder that San Francisco probably should have held onto Daniels and that Harbaugh got snookered by his division rival.

If Daniels succeeds, it will be a rare blemish on Harbaugh's quarterback record.

Read Matthew Barrows' blogs and archives at and listen for his reports Tuesdays on ESPN Radio 1320.

© Copyright The Sacramento Bee. All rights reserved.

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Matt was born in Blacksburg, Va., and attended the University of Virginia. He graduated in 1995, went to Northwestern for a journalism degree a year later, and got his first job at a South Carolina daily in 1997. He joined The Bee as a Metro reporter in 1999 and started covering the 49ers in 2003. His favorite player of all time is Darrell Green.

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