Now there is some hope a new offensive system under Kelly that values mobile quarterbacks could help revive Kaepernick's career if he stays in San Francisco.
"Some of the money that was thrown around at the beginning, you have to be able to manage that," he said. "If you're going to pay some guy who never has been to a Pro Bowl more than anyone on your roster, that's a little bit difficult. There are a lot of things that get involved in this."
After that early success of the Super Bowl run and a trip to the NFC title game the next season, Kaepernick has struggled. He took 52 sacks and saw his passer rating drop from 91.6 in 2013 to 86.4 the following season as the 49ers missed the playoffs in the final year under coach Jim Harbaugh.
Kaepernick went 2-6 in eight starts last season before being benched, raising questions whether the quarterback who led San Francisco to the Super Bowl following the 2012 season was still the man to lead the team.
Things only got worse last year under coach Jim Tomsula. Kaepernick completed just 59 percent of his passes with six TDs,Wholesale Authentic Jerseys, five interceptions and a 78.5 rating before losing his job to Blaine Gabbert midway through the season.
Kelly said he talked to Kaepernick earlier this week and is staying hopeful the mobile quarterback will still be on San Francisco's roster when the offseason program begins April 4.
"He says he's doing well," Kelly said. "He said he feels like he's on track, he's getting healthy and he's excited. That's the biggest thing for him, just getting healthy."
"I'd love to have him. I'm a big Kap fan," Kelly said Thursday after Stanford's pro day.
Despite going 5-11 last season and having plenty of salary cap room available, the 49ers have been relatively quiet this offseason, aside from the speculation about Kaepernick's future. They have signed no prominent free agents,Cheap Jerseys, with their biggest move so far being to re-sign kicker Phil Dawson to a one-year deal. But Kelly said that is all part of the plan he and Baalke have.
First he has to get healthy from medical procedures on his right thumb, his left knee, and on his non-throwing left shoulder to repair a torn labrum. His $11.9 million 2016 contract becomes fully guaranteed April 1 if he's on the roster.

"That was his agents talking to Trent," Kelly said. "I've never been privy to that kind of stuff. I talked to Kap two days ago. A really good conversation. There's a business side of this game. Whatever that it, that is. But if he's here on the 4th, we'll be ready to go."
Last month, Kelly professed his commitment to Kaepernick during the NFL combine,Nike Air Max 98 Og, only to have reports emerge soon after that saying the quarterback's agents had asked general manager Trent Baalke to be traded from San Francisco. The agents haven't responded to multiple inquiries from The Associated Press.
Kelly said he has never gotten that indication from Kaepernick directly,Authentic NFL Jerseys Wholesale.
STANFORD,Cheap Jerseys Wholesale, Calif. (AP) — While others speculate whether Colin Kaepernick wants to remain in San Francisco or if the 49ers still want him as their quarterback, first-year coach Chip Kelly is publicly committed to him.