They might be a man down, too.
After surrendering a staggering 18 sacks in the past three games, the 49ers (10-3) are facing the prospect of playing without left tackle Joe Staley for the Monday night matchup against the Steelers (10-3) at Candlestick Park. The blindside blocker is still recovering from a concussion and hasn't participated in practice this week.
As if San Francisco didn't have enough to worry about.
"You've got to be concerned about everything against Pittsburgh," 49ers offensive coordinator Greg Roman said Friday. "I'm concerned about everything, (their) rush defense is very good. They've got answers for everything."
An offensive line that had shown signs of progress this season has suddenly slipped.
Defenses sacked quarterback Alex Smith 14 times in a three-game span from Weeks 2 to 4, then only seven times over the next six games before he was planted in the turf nine times by the Baltimore Ravens on Thanksgiving night. With the competition improving each week, San Francisco's offensive line has reverted to past form.
Not all of the trouble surfacing is in the passing game, either.
Frank Gore had 10 carries for 72 yards and disappeared in the second half of Sunday's loss at Arizona after scoring a 37-yard touchdown in the third quarter. Smith struggled with a one-sided offensive scheme, although Roman rejected the idea that the team is not striving for balance.
"A couple of weeks ago you guys were complaining that we were running it too much. Now it's flipped the switch, huh?" Roman said. "Every week it's different. The strategies are what they are. Not going to get into strategy. Every week is different. You've got to run it. You've got to throw it. You've got to do both to be successful, short term and long term."
Making matters worse, the patchwork offensive line is still getting pieced together.
Staley, who took a blow to the head against Arizona and didn't return, ran light sprints on the sideline during the portion of Friday's practice open to the media but did not participate with the team. One of the leaders of the line and the 49ers, Staley said he feels fine now but is unsure if he'll be cleared to play.
The left tackle is going through a series of neurological tests this week under the NFL's concussion protocol.
The NFL on Friday denied Harrison's appeal of a one-game suspension for a helmet-to-helmet hit on Cleveland quarterback Colt McCoy, giving San Francisco at least some relief against a blitz-happy defense.
Alex Boone would make his first career start if Staley is inactive, and given the 49ers' recent struggles, he's ready for a lot of disguised pressure from all sides of Pittsburgh's defense.
"I feel like in the NFL when you can't pick up a blitz one time, everyone just hammers you with that same blitz," Boone said. "They just keep throwing it at you and throwing it at you to see if maybe they can get the same thing out of it. So we expect a lot of blitzes, a lot of pressure."
The NFC West-champion 49ers are clinging to the No. 2 seed and a first-round playoff bye -- while New Orleans is making a hard charge -- and can't afford to waste a chance at home in the regular-season finale at Candlestick.
The recent struggles have come on the road, in part, because of crowd noise leading to miscommunication. The 49ers finish the season at Seattle and St. Louis.
And even though San Francisco is preparing for a home game this week, coach Jim Harbaugh pumped in music over the loudspeakers during practice Friday, including the White Stripes, Soundgarden and a variety of hip hop and country music selections -- all in an effort to improve communication.
"Some of it is communication, some of it isn't. Some of it's just we're not getting it done," Smith said of the offense's woes. "It's tough. You're on the road. It's noisy, especially on third down a lot of times. So, it's tough to make calls, hear calls. They're moving around at the last second. All of those things kind of go into it. So, just got to continue to focus and hone in (on) preparation. Things like that all play into that."