Jordan Willis is headed to the IR with a knee injury The 49ers returned to practice Wednesday but were without a few key players. Left tackle Trent Williams sat out due to a veteran’s day off. Linebacker Dre Greenlaw is limited with an elbow injury. Backup offensive lineman Daniel Brunskill continued to sit out with a hamstring injury. George Kittle sat out Wednesday’s practice with a groin injury. Shanahan said Kittle “made a lot of progress” and “hopefully, we’ll have better luck this week” regarding Kittle. On KNBR Tuesday, The Athletic’s Matt Barrows made it sound like it would be…