SANTA CLARA Alex Smith spent January, February and March asking himself the same question: "Is my arm ever going to feel the way it used to?"
The answer, he can say with confidence today, is yes.
The month of June very much belonged to Smith. No, he hasn't moved past Shaun Hill in the competition to be the 49ers' starting quarterback. But he has beaten out Alex Smith of June 2008.
That's the figure that loomed largest in Smith's head.
The Alex Smith of a year ago also was attempting to return from shoulder surgery.
When Dr. James Andrews operated on him in December 2007, Andrews said he didn't know how or why Smith had played three games with the injured appendage. Smith's ligaments that connect the shoulder to the collarbone in a healthy arm were shredded. They were reattached with wires.
Still, Smith was told that his arm would return to full strength in six months. It didn't.
He went through Mike Martz's grueling three-way quarterback competition last summer with what amounted to a phantom limb. His throws never had any zip. His receivers routinely had to reach behind them for the ball. His confidence wobbled.
With that experience in mind, Smith in January began his comeback from his second shoulder surgery, this one to remove a piece of bone that hadn't properly healed from the initial operation.
Once again, doctors reassured him that his arm would bounce back, and they put him on virtually the same rehabilitation regimen he underwent a year earlier.
"So I'm doing the same stuff, and I'm wondering, 'Am I going to come out of this totally 100 percent?' " Smith said. "To go through that (first) surgery and then bust your ass and rehab and then never feel right. "
This time, however, the prognosis proved correct. As May minicamps turned into June organized team activities, there was a certain snap to Smith's throws that observers hadn't seen for two years. The spirals were tight, the throws on target.
That coach Mike Singletary had his players go through two-a-day practices for a stretch earlier this month only bolstered Smith's confidence. His right arm finally had made a triumphant return.
General manager Scot McCloughan recently said Smith looked better than he had at any point in his NFL career. He also is in the best situation of his career.
Mike Nolan, the coach with whom Smith waged a cold war for the past year and a half, is gone. Smith isn't being forced into an offense that doesn't fit his strengths. He reworked his contract earlier this year, and the expectations for him are commensurately more modest.
Smith and Hill also have the best supporting cast offensive line and receivers San Francisco has seen since Jerry Rice and Terrell Owens were in town.
Most of all, Smith has put nearly two years worth of shoulder problems behind him. Now all he must do is elbow past Hill.
Read Matthew Barrows' 49ers blog at www.sacbee.com/ninersblog.


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