Talented Niners still going through changes

The 49ers could again be the most talented team in the weak NFC West this season, but several factors – including a late start because of the NFL lockout, a new coaching staff and the time and repetition needed to learn new offensive and defensive systems and get proficient in them – could prevent San Francisco from getting up to speed as a playoff contender this year before it's too late.

John Madden called young veteran Mike Iupati one of the best guards in the NFL. Left tackle Joe Staley is considered the 49ers' best lineman and the leader of the unit. Yet, against the Houston Texans in San Francisco's third preseason game last week, Iupati and Staley stood frozen in befuddlement while defensive end Antonio Smith slipped between them and crashed into quarterback Alex Smith before Smith could even finish his drop.

That play could be a harbinger for first-year NFL head coach Jim Harbaugh and his team. The 49ers are arguably the most talented team in the weakened NFC West, but it may take them until November or even December before they know what they are doing.

"Knowing where our inside help was, knowing where our outside help was, (was) not tight," Staley said. (There's) a lot of stuff to learn from."

With a new coaching staff calling the shots, the 49ers still are learning everything from the basic to the fine details as they enter Thursday's exhibition season finale at San Diego.

They are huddling differently, and through the first two weeks of training camp, the quarterback snap was frequently botched because centers were learning a new way to hike the ball. In order to learn the changes, coaches worked 18, 20 hours days during training camp, while players frequently put in 15-hour days.

In the end, however, it wasn't enough. The 49ers still find themselves going through changes and behind other NFL teams as the regular season approaches.

"We had to learn the whole package in a timely process and we may never get to the whole package this year because of that," admitted defensive coordinator Vic Fangio, who runs a 3-4 scheme similar to the one the 49ers played last year under new Chargers defensive coordinator Greg Manusky.

So, if the defense will have to wait a year to learn the entire defense, imagine what's happening on offense, where Harbaugh is sweeping out the digital system of the last regime and installing his own complex version of the West Coast offense.

Pile on top of that the tenuous situation at quarterback, the introduction of several new defensive starters, Harbaugh's methodical approach and the fact that's already made for rookie mistakes and the 49ers could be facing another double-digit loss season.

Without much protection, quarterback Alex Smith compiled a passer rating of 33.0 through the first three preseason games. Rookie Colin Kaepernick was only slightly better with 35.1 rating, and he has come off looking exceptionally raw. In all, the two quarterbacks threw six interceptions and no touchdowns in the first three preseason games.

The first-team defense looked impressive in the first two exhibitions, but then struggled to contain the Texans' powerful first-team offense.

That's not surprising since is likely to incorporate seven different starters from last year.

Meanwhile Harbaugh is taking his time in settling his starting lineups. After five weeks of practices and three exhibitions, Harbaugh had yet to settle on his starting center, right guard, or quarterback, although it would a shock if he chose Kaepernick over Smith at that key position.

It's left players to wonder what their roles are going to be, and it's been more difficult to establish continuity with starting jobs still unsettled.

Additionally, Harbaugh's unconventional tactic of playing backups early in the third preseason game against Houston backfired.

The second-team defense allowed long drives, which limited the offense to only 41 plays. Also, the team failed to prepare for the Texans, while Houston treated the game like a regular-season matchup replete with game plans and film study. The disparity in approach led to a 30-7 throttling by the Texans.

Afterward, Harbaugh said the game "did not go as planned."

Unfortunately for him and his team, the regular season may fellow suit.

Niners notes

--- Can you make the club from the tub? That's the question that will surround cornerback Shawntae Spencer (hamstring), wide receiver Crabtree (broken foot), and wide receiver Dominique Zeigler (recovering from knee surgery). Spencer and Crabtree will certainly make the team, however their lingering injuries could prevent them from starting, and neither are expected to play in Thursday's preseason finale. Zeigler is considered to be a terrific special teams player who has reliable hands and who runs clean routes. But his roster spot is threatened by his lack of activity as he only recently returned to full practice.

--- Staley called the performance of the offensive line "disgusting" against Houston. Staley also offered no excuses for allowing Connor Barwin to get three hits on the quarterbacks. "I played terrible," he said.

--- Anthony Dixon's college nickname of "Boobie" is sticking. Players at Mississippi State started calling him Boobie after the big back showcased his quick feet, receiving ability and even his passing acumen as a freshman. His abilities reminded him of the star player in the movie, "Friday Night Lights."

--- Dixon also has two younger players playing minor league baseball, including an outfielder Rashaun, who plays for the Oakland A's single-A team in Stockton. Dixon often drives the 90 minutes to see his brother play. "He struck out twice the other night. I had to get on him a little bit," Dixon said.

--- Rookie wide receiver Ronald Johnson is so dedicated, the former USC player takes a football wherever he goes. He even straps into the passer side seat when he's driving. He has also written on the ball the word, "Baby."

--- Harbaugh refuses to wash his blue pickup truck, because that would destroy a spider's web clinging to Harbaugh's sideview mirror. Harbaugh has been so interested in the spider, he even googled spiders to see how long they live. Harbaugh even admits he talks to his little friend. He admitted recently that he has not seen the spider in about a week, but is hopeful a new one will inherit the web. It goes to show what sleep deprivation will do to you. "I haven't washed the truck yet, so maybe there will be new spiders that emerge." Harbaugh said.

--- Cornerback Phillip Adams spent his off-season rehabilitating from a gruesome broken ankle he sustained last year in St. Louis on Dec. 26. He decided to do it at home with his parents in Rock Hill, South Carolina to be close to his mom, who lost the use of her legs in a car accident two years ago. His mother is also rehabilitating and hopes to walk again. "We compared notes at the end of the day," Adams said about their daily rehab sessions.

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