Jim Harbaugh loves to tell us (the media, fans, and probably his own players when no one else is around) to “assume nothing.” So it almost makes sense that, with the Miami Dolphins sporting one of the better rush defenses while also allowing 258 passing yards per contest, the 49ers would find their greatest success on the ground.

The 49ers’ defense was good, not great. Chris Culliver looks like one of the best cornerbacks in the league, Patrick Willis was his usual active and punishing self, and Aldon Smith picked up his second sack late after passing Fred Dean for the franchise record in the second quarter. That gives Smith 19.5 on the season, which means if he can come up with 3.5 sacks in his last three games, he’ll break Michael Strahan’s all-time record.

However, the story coming out of this game revolves around the offense … again. While they scored 27 points against a pretty decent defense, there will be questions.

Was it an above average offensive afternoon when one of the touchdowns was set up by Marcus Thigpen muffing that punt near his own goal line?

Why did the 49ers have so much trouble converting on third down?

Why are there so many instances when the play clock runs down to zero, forcing the 49ers to take timeouts?

Where’s Vernon Davis, who, after blowing up against the Bears for 6 catches, 83 yards and a touchdown in Colin Kaepernick’s first start, has only caught three balls for 19 yards in the three games since?

The good news for San Francisco was their offense answered the biggest question coming out of the overtime loss in St. Louis: have teams found out how to stop the Frank Gore and the rest of the 49ers’ rushing attack?

Unless you’re talking about teams coached by Jeff Fisher, the answer to that last question is NO.

The Dolphins came in allowing only 3.7 yards per carry, and the 49ers had 158 yards on 28 carries (5.5 ypc, which was inflated by a certain read option run). More importantly, they scored three rushing touchdowns. Before today, the Dolphins had only allowed five TDs on the ground.

Gore gained 5 more yards against Miami than he did in St. Louis … on 11 fewer carries. Shouldering some of the load was rookie LaMichael James, who it’s safe to say will no longer find himself on the inactive list after collecting three first downs (two on the ground, the other on a 15-yard reception). Also, the run blocking was about 200% better this week, although Alex Boone hit Gore as hard as any Dolphin did on the afternoon.

“He keeps tackling me,” Gore said in the video below, one of two funny moments from his postgame press conference. “I told him, ‘You got to stay off me, man. Let me get another touchdown.'”

The starting quarterback, Sergio Romo makes an appearance, and other notes…

— It isn’t really worth it to transcribe Colin Kaepernick’s short answers during postgame pressers, but here are some things I noticed today:

  • His deep pass to Randy Moss on the flea flicker was right on the money. With a defender draped across Moss’ right arm, the catch wasn’t an easy one to make … but he might have made it a few years ago.
  • Kaepernick’s accuracy is pretty outstanding, but his awareness of the clock has to improve.
  • He could also stand to hurl the ball a teensy bit softer on close-range passes.
  • It’s hard to imagine a quarterback who turns the corner faster while running left. Once he broke through the first level on that 50-yard TD run, he looked like Usain Bolt.
  • In all, Kaepernick had a very similar game to what we’d expect from Alex Smith. Not that great on third down, completed most of his passes (78.3%), no turnovers (partly because Anthony Davis recovered Kaepernick’s fumble).

— Harbaugh indirectly fired back at Greg Roman’s critics after the game.

“Yeah, great call by Greg,” Harbaugh said in response to the first question of the press conference, about Kaepernick’s long TD run on a read option play.

“I thought Greg called a great game. He always does,” Harbaugh said a few minutes later.

— Frank Gore on his sixth 1,000-yard season and his outstanding durability and production at an advanced age, at least for a running back: “When you see everybody say when you turn 29, 30, you can’t do it anymore. When I got to 29 I told myself I was going to overcome that. It’s all about training in the off-season. Being smart during the week, that’s something Tom Rathman does a great job with me.”

— James said he didn’t have any butterflies when he went back to return his first NFL kickoff. “That really surprised me. I really wasn’t nervous at all,” he said. Here’s the rest of his answer to that question:

— Donte Whitner’s body-slam of Reggie Bush had everyone making wrestling references for a while.

— Whitner also came to the podium in one of the gold retro 49ers jackets that are back on sale.

— Michael Crabtree had a very busy day, catching 9 passes for 93 yards. Almost half of Kaepernick’s passes went in Crabtree’s direction, as he was targeted 11 times.

— Sergio Romo was in this day’s celebrity guest (a la Owen Wilson and Vince Vaughn during the game against the Lions), and was in the locker room afterward with a signed football. I talked to him for a bit while he picked up autographs from Vernon Davis and Anthony Dixon; I should have that interview up by tomorrow morning.

Bruce Miller isn’t just the best blocking fullback in football, he may also be the nicest. When James was talking to reporters, someone brushed past me (it might have been Miller). I felt a tap on my shoulder, and Miller (wearing a towel) hands me the lens cap to my camera, which must have gotten knocked off by whoever walked by. I’m having a hard time thinking of any other professional athlete who would grab something off the floor and hand it to a media guy they don’t know. Romo, maybe.

— Gore was wearing a unique sweatshirt, one with a different take on the Dolphins logo. In it, the dolphin was upside down with X’d out eyes. Someone asked him about it at the end of his press conference, and here is what he said:

“I said we gotta flip ’em upside down when we play them.” Brilliant.

— Gore was also wearing some Reebok Pumps with hot pink accents that look like something Brian Wilson might wear, and they matched perfectly with his sweatshirt. I didn’t get a photo of Gore’s shoes, but here’s a shot of the upside down dolphin.