SANTA CLARA, Calif. -- Vernon Davis had a cross-country flight and an entire off day to think about the touchdown that should have been.
Colin Kaepernick overthrew the tight end on a would-be 34-yard score during the first quarter of Sunday's 41-34 victory at New England.
Davis acknowledges he is still getting used to Kaepernick, who is 4-1 since becoming the starter in place of Alex Smith and earned NFC Offensive Player of the Week honors after the upset of the Patriots.
"I get chills when I think about it," Davis said of the missed opportunities. "One thing I learned in the beginning when I first got here, everyone was talking about being on the same page as the quarterback, as Alex Smith. You have to develop that chemistry, that bond so you can be on the same page. That's something me and Kap don't have right now. We don't have it; you have to expect it because he just stepped in."
From gauging the zip on the ball after its release to learning the tendencies of the strong-armed Kaepernick and finding their timing together, Davis said he believes things will soon start clicking.
Another special January would be just what Davis has in mind. He caught the winning TD from Smith to beat New Orleans 36-32 in last season's divisional playoffs, then had touchdown receptions of 73 and 28 yards in a 20-17 overtime loss to the New York Giants in the NFC title game.
If they can get on the same page Sunday night at Seattle, that would be even better as far as Davis is concerned. The Niners (10-3-1) can clinch a second consecutive NFC West title with a win, and they're also determined to keep hold on the No. 2 seed -- and a first-round playoff bye that would come with it -- by slowing down the red-hot Seahawks (9-5).
Davis has only 39 catches for 516 yards and five touchdowns this season, with just four receptions over the past four games after getting a season-best six in a Monday night win against the Bears on Nov. 19. He had one catch for 10 yards at New England.
Coach Jim Harbaugh has repeatedly said a big part of deciding whether to target Davis has to do with the swarming defense and double coverage he draws.
Harbaugh is pleased with the extra work Davis and Kaepernick are putting in after practice.
"I can think of a couple things in particular where Vernon and Colin spent some extra time on certain routes, extra during and after practice, and that helped," Harbaugh said Wednesday. "Just specific plays. That was a positive for us and that's something we can continue. ... I think there will be some more focus on that this week."
Of the near misses in Sunday's win, Harbaugh said those might be fixed with "maybe some more time on task, just between the two of them."
Kaepernick and wideout Michael Crabtree have quite the connection going already, but now Davis is determined to find it, too.
"Just extra throws," Kaepernick said, expanding only by saying, "we're making progress because we're getting those extra throws after practice."
Not that Davis and Smith had a rhythm right away.
It was the 2009 season when Davis led the 49ers with 78 catches for 965 yards and 13 touchdowns, which matched Antonio Gates' NFL record for TDs by a tight end. Davis made his first Pro Bowl that year and tied for the league lead in touchdown catches with Randy Moss and Larry Fitzgerald.
"It took a while, but with Kap I'm sure if we just continue to rehearse and work on it, we can make it happen," Davis said. "He's a fast learner, just like Alex. But it takes time."
Davis is quick to credit Crabtree for the way he is running his routes and for getting open.
"It depends on what your routes are," Davis said. "The routes, speed, all those things come into consideration."
With the next game being in the NFL's loudest venue, keeping up with Kaepernick becomes that much more important. The 49ers spend time in practice trying to simulate the crowd noise, though that's tough to do.
"One thing we've got to work on is getting in the huddle and watching his mouth as he calls the play," tight end Delanie Walker said Wednesday.
Kaepernick and center Jonathan Goodwin are still finding their groove, too.
They struggled on their exchanges against the Patriots, and Kaepernick fumbled four snaps. Of course, the conditions were wet.
"Don't ask Goody about it. It's my fault," Kaepernick said aloud in the locker room Tuesday.
To which Goodwin replied: "No, it's 50/50, like a husband and wife."
DT Justin Smith didn't practice during the open portion of Wednesday's workout. Harbaugh remains optimistic he can go Sunday -- which would be Smith's 186th consecutive start. "If it's humanly possible," Harbaugh said. "We'll see how he feels today and tomorrow." ... WR Mario Manningham wore a non-contact black jersey as he nurses a right shoulder injury that has sidelined him for the past two games. ... For anyone thinking Harbaugh changed up his standard uniform at New England, he said: "Khakis were underneath. It was a rain suit over the khakis."