Since we're piling on kudos for the defense, I might as well add another.
Up to the middle of the second quarter, Kaepernick had scrambles and called runs for 12, 9, 3, 4 (called back for holding), 17 (reduced to 10 yards on a penalty), and 14 yards with 0 sacks.
From the 6 minute mark of the second quarter, starting with the Perry/Elliott back-to-back red zone sacks, the scrambles and runs were 3, -1, 7 and 5 yards with 6 sacks.
Adjustments were made, something that's been largely missing over the past 4 season, and it didn't even take until halftime. Further, what you didn't see in the SF game was the level of pursuit and gang tackling in the earlier games with evidently greater assignment discipline, appropriate to the opponent. That wouldn't work unless guys are making one-on-one tackles or at least solid hits until support arrives.
It's still early, and unqualified praise one week has a bad habit of looking foolish the next, but this defense is working it's way toward a balance of coherence and aggression that one can't help but like.