Roster set, but questions remain for 49ers

There are just four days until 49er football returns, so what better time to revive this blog, which has been dormant for quite some time.

After a long offseason dominated by off-the-field story lines, a training camp blighted by injuries, and four preseason games, the 49ers' 53-man roster is set.

Heading into Sunday's clash with the Dallas Cowboys, here's how the 49ers' roster has taken shape.

QB: Colin Kaepernick, Blaine Gabbert, Josh Johnson
RB: Frank Gore, Carlos Hyde, LaMichael James
FB: Bruce Miller
WR: Michael Crabtree, Anquan Boldin, Steve Johnson, Brandon Lloyd, Quinton Patton, Bruce Ellington, Kassim Osgood
TE: Vernon Davis, Vance McDonald, Derek Carrier
OT: Anthony Davis, Joe Staley, Jonathan Martin
OG: Alex Boone*, Mike Iupati, Joe Looney, Dillon Farrell
C: Daniel Kilgore, Marcus Martin
DT: Justin Smith, Ray McDonald, Tony Jerod-Eddie, Demarcus Dobbs, Tank Carradine, Quinton Dial
NT: Ian Williams
OLB: Ahmad Brooks, Corey Lemonier, Dan Skuta, Aaron Lynch
ILB: Patrick Willis, Michael Wilhoite, Nick Moody, Chris Borland
CB: Tramaine Brock, Chris Culliver, Jimmie Ward, Perrish Cox, Chris Cook, Dontae Johnson
S: Eric Reid, Antoine Bethea, Craig Dahl, L.J. McCray
K: Phil Dawson
P: Andy Lee
LS: Kyle Nelson

*The 49ers have applied for a roster exemption for Alex Boone following the end of his holdout

Practice Squad: Carter Bykowski, Chance Casey, Asante Cleveland, John Fullington, Kendall Gaskins, Lance Lewis, Lawrence Okoye, Mike Purcell, Shayne Skov, Chase Thomas
Injured Reserve: Kenneth Acker, Kendall Hunter, Chuck Jacobs, Will Tukuafu
Injured Reserve/Designated for Return List: Glenn Dorsey
Physically Unable to Perform: NaVorro Bowman, Garrett Celek, Kaleb Ramsey
Reserve/Non-Football Injury: Marcus Lattimore, Trey Millard, Keith Reaser, Brandon Thomas
Reserve/Suspended: Aldon Smith

There were a few surprises in the 49ers' final round of roster cuts, which were survived by Josh Johnson as San Francisco unexpectedly decided to go with three quarterbacks on the roster after an impressive preseason campaign from the former Tampa Bay Buccaneer.

Wide receiver Brandon Lloyd - who returned to the 49ers following a year away from the game - made the team despite barely featuring in preseason, while fellow wideout Steve Johnson will need to show improvement after struggling to build a rapport with quarterback Colin Kaepernick.

On the defensive side of the ball Michael Wilhoite appears to have won the competition to replace NaVorro Bowman at inside linebacker and cornerback Chris Cook, who recorded two interceptions in preseason, impressed enough to make the roster.

L.J McCray - an undrafted free agent out of Catawba - stunned everyone by beating out special teams veterans C.J. Spillman and Bubba Ventrone to earn a place on the 53.

However, long snapper Kevin McDermott was unable to keep his place on the squad, with Kyle Nelson, who can also operate as a tight end, taking the job from him thanks to a two-touchdown performance in the preseason finale with the Houston Texans.

The Niners are still regarded as one of the top contenders for this season's Super Bowl but, while their roster is evidently stacked with talent, they have a fair share of issues to overcome if Jim Harbaugh's men are to make the dream of a sixth NFL title a reality.

Most of those concerns surround a previously much vaunted defense that will be lacking a number of other key components as well as injured All-Pro Bowman.

Indeed, with Aldon Smith sidelined for nine games after being suspended by the league for his various off-the-field indiscretions, the Niners will once again need the likes of Dan Skuta and Corey Lemonier to step up and perform after doing so when Smith missed five games in the 2013 campaign.

The presence of exciting fifth-round pick Aaron Lynch may also help the 49ers cope without Smith's considerable talents as a pass rusher, yet the 49ers' problems recently mounted further with the news that Ray McDonald was arrested on Sunday on domestic violence charges.

San Francisco will allow the legal process to run its course before making a decision on McDonald's long-term future, but they now face a dilemma over whether to play him against Dallas so soon after the reported incident.

Last season in the aftermath of Smith's DUI, the 49ers made the wrong decision in opting to play him.

That call backfired as he produced a sluggish performance in a humbling at the hands of the Indianapolis Colts.

The two situations are not exactly the same but the Niners must think more carefully than they appeared to do with Smith, and decide whether the likes of Tony Jerod-Eddie, Quinton Dial and Tank Carradine are good enough to allow them to bench McDonald and send a message to the team and the NFL about their attitude to such instances of apparent misconduct.

On offense things look much rosier now guard Alex Boone has ended his prolonged holdout.

Boone's presence should shore up an offensive line that looked shaky in preseason, however, with the defense seemingly weakened, it will be interesting to see if the offense can handle the presumed extra pressure on their shoulders and put the points on the board to keep the Niners in the Super Bowl hunt.