DENVER – After his second look at Peyton Manning this offseason, Jim Harbaugh should have no doubt: The quarterback's surgically repaired neck is just fine.

The condition of Harbaugh's first-team defense, however, is more iffy.

The unit, which finished second in points allowed last season, offered little resistance as Manning's three drives resulted in a 17-0 Broncos lead. The 49ers' second- and third-stringers came back in the second half for a 29-24 win, but there was concern afterward that a 49ers defense that dominated in 2011 has been merely so-so this summer.

"There was some spotty play," Harbaugh said afterward. "And we gave up some easy yardage and found ourselves, for whatever reason, not in good football position when it came to making an attack or a breakup … so fundamental-type things that we need to look at."

Harbaugh noted that key players from the defense have been missing through the first three exhibition games. Starting linebackers Aldon Smith and NaVorro Bowman, for example, sat out Sunday's game with injuries that are not expected to last until the regular-season opener.

Manning and his new favorite target, wideout Eric Decker, scored the first touchdown of the exhibition season against the 49ers' first-string unit.

But opponents have been marching down the field since the 49ers' Aug. 10 exhibition opener. Six of the seven drives against San Francisco's top unit have resulted in scores. The 49ers' starters have no sacks and have forced no turnovers.

And opposing quarterbacks – Christian Ponder, Matt Schaub and Manning – have combined for a 121.3 passer rating. Manning was 10 of 12 for 122 yards in one quarter of play.

The 49ers will face a virtual all-star lineup of quarterbacks this season, beginning with Green Bay's Aaron Rodgers in Week 1.

Starting linebacker Ahmad Brooks conceded the 49ers were off to "a scary start." But he also noted that while the 49ers have not had more than a cursory game plan for their preseason opponents, they and the coaches have been looking at Rodgers and the Packers for months.

"I wouldn't be too concerned with it," Brooks said. "We have some guys out right now. … If we can just game-plan for the offense, we will do better on the defensive side of the ball."

On offense, meanwhile, Alex Smith and the first-string team went three-and-out on their first series, fumbled away a snap on the second but responded with perhaps the 49ers' best pass play this summer.

After a surprise onside kick by Denver was called back on a penalty, Smith found Vernon Davis being tightly covered by linebacker Von Miller, then hit Davis in stride for a 44-yard touchdown as the tight end blew past the defense.

"We're so far ahead of the curve than we were a year ago," Smith said. "And building off that doesn't guarantee you anything, but it is definitely nice. We're able to get more detailed with the things we are doing."

Quarterback Colin Kaepernick had a strong game in going 4 of 4 for 80 yards and rushing twice for 11 yards. Kaepernick, who played the third quarter, connected with Kyle Williams for a 46-yard catch-and-run play, the 49ers' longest pass play of the preseason and a pass described by Harbaugh as "a laser."

Kaepernick also had an impressive throw to tight end Konrad Reuland while rolling to his left away from pressure. Harbaugh said Kaepernick played better from the pocket than he had in the first two games.

"I thought he played with poise, and he was cool," Harbaugh said. "I thought it was a positive step for Colin."

Scott Tolzien entered the game after Kaepernick left. Josh Johnson came in late in the fourth quarter. Harbaugh, however, did not offer any hint concerning who was ahead in the competition to be the No. 3 quarterback or if the 49ers had fielded any trade offers.

"It's still playing out," Harbaugh said.

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