On defense, they were missing All-Pro linebacker Patrick Willis (toe), starting cornerback Chris Culliver (hamstring) and No. 3 cornerback Jimmie Ward (quadriceps), and cornerback Chris Cook (hamstring) exited in the third quarter. On offense, they were without All-Pro guard Mike Iupati (concussion) and lost center Daniel Kilgore to a season-ending broken ankle in the second half. [...] this doesn’t include their players coming off injuries who operated at what appeared to be less than full strength: tight end Vernon Davis (two catches, 21 yards) and cornerback Tramaine Brock, who was beaten on two of Peyton Manning’s four touchdown passes. Some of those key guys, however, are expected to be ready after the bye for a home game against the Rams on Nov.