Kirk, the former Etowah High School and University of Georgia star, was 9-under par, and played his last few holes just as the wind picked up in the afternoon and made scoring more difficult. Kim and Wagner took advantage of calm morning conditions. Kim shot a 64, the lowest round of the day, and Wagner had a 67.
"I've got very good feelings as soon as I step on the property here," Wagner said.
Padraig Harrington, first-round leader Jimmy Walker and Josh Teater were two shots back at 7 under.
Organizers groomed the Tournament Course at Redstone to simulate conditions that players will see at the Masters next week, and the set-up lured many of the world's top players to Houston.
Phil Mickelson (70) and Lee Westwood (72) were part of a large group at 4 under and Ernie Els (72) and Fred Couples (72) were among the players at 1 under.
The cut fell at even par, and former Masters champions Jose Maria Olazabal and Angel Cabrera were among those who failed to qualify for the weekend.
Kirk, second on the Nationwide Tour money list last year, birdied two of his last three holes to take the outright lead and make up for a double bogey on the par-5 fyourth.
"I made one bad swing off the tee, and it wasn't even really that bad," Kirk said. "One of those things. No matter how good you're playing, that kind of stuff happens sometimes."
Kim's 64 was four shots better than his lowest round when he won last year.
Starting on the back nine, Kim made six birdies in his first 10 holes, including chip-ins on Nos. 12 and 16. He needed only 22 putts to equal his lowest round since January.
Kim said before the tournament that his swing needed major retooling and that he spent several days working with coach Adam Schreiber on changes. He's gratified that the work is already producing results.
"It's been a tough stretch," he said, "but I'm glad to have this one (round) under my belt and now I can draw back on this and know that when I get it going, I can shoot under par."
And it certainly helps that he's back at one of his favorite courses.
Before Kim turned pro, he won a collegiate event here in 2006. He tied for fifth as a tour rookie in 2007 and shot three sub-70 rounds last year to win.
"It helps, knowing I played well before, knowing I made a couple putts when it mattered," he said. "Some shots I had are similar, some putts I had are very similar, so I try to remember those things, and play off that."
Wagner earned his first tour victory here three years ago, then tied for 36th at his first and only Masters the following week. He needs to win this week to qualify for Augusta again, but says next week's major has hardly crossed his mind.
A Charlotte, N.C., resident, Wagner personally ranks the tournament at Quail Hollow near his home and the Houston event as important as any tournaments all year in his mind.
"There are a few regular tour events that I treat as a major," he said. "Houston and Charlotte will always be my two favorite events that we play."
Harrington seems to like it, too. He's played here every year since the event moved to the Tournament Course at Redstone and finished in the top 40 each time.
He opened with a 68 on Thursday, then birdied two of his first three holes in the placid morning conditions on Friday. Also starting on the back nine, he hit his tee shot into the bunker on the par-3 14th and bogeyed, but then holed birdie putts on 16 and 17 to reach 8 under.
Harrington dropped back with three straight bogeys on his back nine, then reached the par-5 eighth in two shots to set up an eagle to get back to 7 under.
"I just fell asleep there," said Harrington, sporting a beard this weekend because he forgot to pack a razor. "I really kind of battened down the hatches for the last couple of holes, trying to not make too many mistakes after I lost my way."
Walker struggled to a 74 after tying the course record with a 63 on Thursday. He dunked his tee shot in the pond on No. 11 on Friday and took a double bogey, and made only one birdie the rest of the way.
Former President George H.W. Bush watched the early rounds from a golf cart and greeted Mickelson and Couples as they walked off greens. Bush regularly attends major sporting events in Houston, where he lives.