NFL Draft: Could a Prince solve secondary woes?

We’re on the clock. We’re in two-digit territory.

Yes, it’s only 99 days until the NFL Draft.

Never mind that the 49ers’ regular season spanned 113 days, it’s time to launch into Mel Kiper mode.

By the time Roger Goodell announces the No. 1 overall pick, we’ll be able to pronounce Prince Amukamara, tick off Von Miller’s time in the three-cone drill and compute the average Wonderlic score of Blaine Gabbert, Cam Newton and Pat Devlin faster than you can say “blue-chipper with a high-end motor and a huge ceiling.”

In his interview on KNBR last week, general manager Trent Baalke was asked about the upcoming draft. Baalke responded to questions about the Niners’ three biggest areas of perceived need: Quarterback, cornerback and pass-rusher, presumably an outside linebacker.

We’ll start with the cornerback position.

And away we go:

CORNERBACK

WHY IT’S A NEED: Cornerbacks Nate Clements and Shawntae Spencer were part of a pass defense that ranked 24th in the NFL and tied for 17th in interceptions with 15, six coming from the front seven.

Clements and Spencer combined for six interceptions, two fewer than Baltimore safety Ed Reed and just three more than Green Bay cornerback Tramon Williams has collected in two playoff games.

The Niners were stout against the run. They ranked second in the NFL in yards per carry (3.5), sixth in yards allowed (96.7) and were one of two teams to not allow a 100-yard rusher (Pittsburgh).

But they were repeatedly undone by their inability to contain high-end passers.

Consider: The 49ers were 0-6 against quarterbacks who finished the season ranked among the top 12 in the NFL in passer rating. They were 6-4 in other games.

Those six quarterbacks (Philip Rivers, Aaron Rodgers, Josh Freeman, Matt Cassel, Matt Ryan and Drew Brees) completed 67.2 percent of their passes (123 of 183), threw 14 touchdowns and three interceptions and posted a passer rating of 110.6. In those six games, the Niners were outscored 161-69 (they outscored their opponents 236-185 in their other 10 games).

Think a lockdown corner could make a difference?

Clements, 31, who could earn more than $15 million in base salary and incentives in 2011, won’t return unless he takes a pay cut, according to CSN Bay Area. And the backups at the position – Tarell Brown, Will James, Tramaine Brock and Phillip Adams – haven’t established themselves as starter material.

WHAT BAALKE SAYS: Baalke noted that it’s possible to draft a cornerback and turn him into an instant starter. He pointed to New England rookie Devin McCourty, who tied for second in the NFL with seven interceptions this past season. McCourty was a first-round pick (27th overall) from Rutgers.

“They’re out there,” Baalke said. “You’ve got to find them. The whole thing to playing that position is confidence. Obviously they have to have the physical ability to do it, but they have to be put in position to make plays and they have to be coached to make plays. And they’ve got to have confidence about them.”

After highlighting the importance of confidence, Baalke noted a slight problem with the Niners’ corners this past season: They played tentatively.

“I think if you talked to our guys, they lost a little bit of (confidence),” Baalke said. “For whatever reason, they lost some of that — that play-making, that mindset to make plays rather than to just not get beat. And that’s a position that gets exposed. Everyone sees when they make a mistake or when they make a good play. Everyone sees it … When they make a mistake, it’s there for the world to see and when they lose confidence in their ability to make those plays is when they start playing soft and when they start giving up things that they normally wouldn’t give up.”

Of course, the corners weren’t helped by the Niners’ inability to generate a consistent pass rush. In the aforementioned six games against top-12 quarterbacks, San Francisco managed 12 sacks.

The corners, obviously, would benefit from an effective pass-rusher, who could harass a quarterback and mask breakdowns in coverage. And a lockdown cornerback could allow defensive coordinator Vic Fangio to get more creative in the ways he brought pressure.

“Obviously, if you get a shutdown corner it allows you to do some things defensively and put more pressure on a defense, blitzing, doing things like that. Utilizing more guys to get to the (quarterback),” Baalke said. “But by the same token we want to be balanced. We want to be able to get a four-man rush. We want to be able to play coverage.”

WITH THE SEVENTH PICK IN THE 2011 NFL DRAFT …: The good news: There are two elite cornerbacks in the draft.

The bad news: LSU’s Patrick Peterson and Nebraska’s Prince Amukamara are so highly regarded the Niners might not be in a position to get them at No. 7.

Peterson (6-1, 211) won the Bednarik Award (nation’s best defensive player), the Thorpe Award (top defensive back) and was named the SEC’s Defensive Player of the Year as a junior this past season when he also began returning punts and kickoffs. In his first game against North Carolina, he had 257 return yards, which ranks second in SEC history.

The point? He’s good. So good that it’s possible the Broncos take him with the No. 2 pick with free-agent cornerback Champ Bailey, 32, entering his 13th season.

Amukamara (6-0, 203), 21, was named the Big 12 Defensive Player of the Year as a senior this past season.

Ask two of the top quarterback prospects about Amukamara, who headlined a secondary that shut down Washington’s Jake Locker and Missouri’s Blaine Gabbert in 2010. Locker completed 4 of 20 passes in a 56-21 loss to Nebraska and Gabbert completed 18 of 42 passes in a 31-17 loss to the Cornhuskers.

After Peterson and Amukamara, the next cornerback on the board could be Miami’s Brandon Harris, who is being viewed as a late first-round selection.

WHAT THE DRAFTNIKS SAY: In his first mock draft, Mel Kiper has the Broncos taking Peterson at No. 2 and the Cowboys selecting Amukamara at No. 9.

Scouts Inc. ranks Peterson No. 3 and Amukamara No. 5 among its top 32 prospects.

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