The 49ers and Alex Smith finally agreed to terms on a contract, ending the 49ers’ suddenly turbulent search for their 2012 quarterback. Many may concur with the idea that Smith still has much to prove – seven years of failure is not easily forgiven, even after a season of success.

Although the 49ers may still invite Buccaneers free agent back-up quarterback Josh Johnson for a look, it appears the position of quarterback is finally set.  Smith is the 49ers quarterback for 2012, with Colin Kaepernick spending another season in the wings.  What they do with Scott Tolzien is anybody’s guess – he’ll probably stay put unless Jim Harbaugh’s still crushing on Johnson.

Enough about the quarterbacks. What about the team, the team, the team?

The 49ers bolstered their receiving corps, adding Randy Moss on a “prove it to us” deal and Mario Manningham on a mysterious 2-year contract (the details of Manningham’s deal slid under the “where the hell is Peyton going to play” radar). Incumbent wideouts Michael Crabtree and Kyle Williams will be back, while it’s beginning to look like Ted Ginn will be taking his questionable hands elsewhere.

The 49ers signed former Raiders special teams ace Rock Cartwright, presumably to replace Blake Costanzo, who signed with Chicago. They also added secondary depth by signing Parrish Cox to a 2-year deal. The re-signed Ahmad Brooks to a 5-year deal, solidifying Aldon Smith’s counterpart and instilling faith in the once-troubled outside linebacker. But arguably their biggest pick up was wooing Carlos Rogers back on an affordable 4-year contract.

Where are the holes?

Position to position, there really aren’t many.

Defensive Backs – With Rogers, Chris Culliver, Tarell Brown, Cox and Tramaine Brock, the 49ers have a pretty solid core of young cornerbacks. But the key word there is YOUNG – they may still be in the market for some corner help.  There’s no telling what the 49ers have in Cox, who’s been involved in more than a few off the field incidents. The NFL Draft is a likelier source if the 49ers want to add cornerback depth, but they might wait out the market and add a CB who falls through the cracks.

The 49ers are solidified at free and strong safety with Dashon Goldson and Donte Whitner.  The drop off should one of them get hurt is significant, especially with names like Colin Jones, CJ Spillman and Mark LeGree as your backups. Adding a safety in free agency or the later rounds in the draft is a possibility.

Linebackers – Not much to complain about here.  The 49ers have the best inside linebacker duo in the league between Navarro Bowman and Patrick Willis.  They just re-signed Ahmad Brooks to a hefty 5 year contract and Parys Haralson is still around … for now.

Defensive Line – Not much to be done here either.  Justin Smith and Aldon Smith should anchor both sides, although Aldon’s also known as an OLB.  With Ray McDonald and Isaac Sopoaga clogging up the middle, stuffing the A and B gaps shouldn’t be a problem.  With Ricky-Jean Francois and Ian Williams also in the mix, the 49ers should be well-equipped to handle opposing offensive lines next season.

Special Teams – David Akers and Andy Lee are back, which means the 49ers remain strong in the legs.  Always-trusty Brian Jennings should still be the team’s long snapper, but recently signed Ryan Pontbriand and Kyle Nelson will provide competition. Most of the special teams crew from 2011 is back, sans Costanzo. Without him the #TonyMontanaSquad is probably retired forever. Perhaps Boobie Dixon has something up his sleeve?

The 49ers have a void in the return game. Fans probably won’t ever warm up to the idea of Kyle Williams as a return man, and though Delanie Walker and Rock Cartwright can do it, they’d be a huge downgrade from what Ginn provided.

Quarterback – Smith re-signed, Kaepernick’s still learning and Tolzein’s around in case of emergency. Will the 49ers sign Johnson? That option seemed a lot more tempting a year ago.

Running Back – Frank Gore looks like the man going forward, with Kendall Hunter giving him a break as a true change-of-pace back. I like Hunter as a role player, but I don’t envision him as the every down halfback that Gore has been for so long. Bruce Miller has turned out to be an incredible pick up by Trent Baalke, so fullback is set as long as he stays healthy.  Anthony Dixon is the Flava Flav of the 49ers – one hell of a hype man, but not much else. It would be wise to find a reinforcement at this position, as Gore’s nearing the end.

Wide Receiver – This is a chicken and egg situation – do just-okay wide receivers make Alex Smith just-okay, or vice versa?  With the 49ers adding Moss and Manningham to complement Crabtree and Williams, adding Mike Wallace is unlikely. However, drafting a wide receiver isn’t.

Tight ends – If Vernon Davis and Delanie Walker aren’t good enough for you, you’ve got some mighty high standards.  On the other hand, many would love to see Coby Fleener in red and gold.

Offensive Line – Here’s the only spot left on the roster that truly needs help. Geoff Schwartz showed up in Santa Clara on Tuesday to have a a meet and greet with the 49ers. Schwartz, 25, grew up a 49ers fan.  Originally drafted in the seventh round in 2008, Schwartz started all 16 for the Panthers in 2010 before missing 2011 due to a hip injury. Veteran Leonard Davis is also an option.

The rest of the offensive line looks solid. Anthony Davis is young and filter-less (at least when it comes to Twitter) but he seems to be progressing at right tackle. Joe Staley comes off a year where he was named 2nd-team All-Pro, Mike Iupati didn’t get the same recognition but was just as effective, and Jonathan Goodwin was a nice addition. The other guard spot remains the wild card, with Daniel Kilgore and a yet-to-be-signed player probably competing for the job.

After taking a step back, the amount of time it took Harbaugh and Baalke to solidify this team is stunning. Once the pieces are in place, the real fun begins: resuming the ever-entertaining chemistry experiment that is coaching up Alex Smith.