Fooch's Update: PFT tweeted out just after 1 p.m. PT that the surgery finished and went well.
It would appear Bowman is getting his ACL repaired, and will be ready to begin his recovery and rehab process. Matt Maiocco tweeted that world-renowned orthopedic surgeon Dr. James Andrews is handling the procedure in Pensacola, Florida.
Bowman tore his ACL in the NFC Championship Game, and suffered additional damage to his MCL. The initial belief was that both ligaments were fully torn, but it sounds like the MCL damage was only a partial tear. Bowman's surgery was delayed so that the MCL could heal. This is excellent news for his recovery.
Socalisteph will provide more details in the coming days, but simply put, having only a partial tear of the MCL means there is more stability for his ACL recovery. Had he fully torn both ligaments, the rehab would have been longer in part because the stability of the knee would be that much less. We saw this issue in part with Mario Manningham's recovery from a torn ACL and PCL. The PCL is not the same as the MCL, but stability remained an issue. It is possible surgery might reveal more than the MRI showed, but we remain optimistic.
The recovery process is in the 6-8 months range. It is conceivable for Bowman to get back for the start of the 2014 regular season, but we'll have to wait and see how his recovery develops. I suspect he starts training camp on the PUP list. Then, he either starts the regular season on the PUP list, or the team activates him at the end of camp and he is inactive for a few weeks to start the season. My guess is the former, but the latter remains a possibility.
Whenever he returns, in the meantime, Michael Wilhoite will get first team snaps next to Patrick Willis. Wilhoite is an exclusive rights free agent, which means he will be re-signed, likely at a veteran minimum one-year contract. He is a free agent only in the sense that he can choose to not sign with the 49ers. If he chose that option, he would have to sit out of the NFL, so obviously that won't be happening.
Wilhoite did solid work briefly filling in for Patrick Willis, and I expect nothing less when he fills in for Bowman. This will also give Willis a chance to show the world that he is still one of the best linebackers in the NFL. I think most of us know that, but he started to slip under the radar a bit as Bowman has emerged the last two seasons. I expect big things from Willis while Bowman is sidelined.