Symptom Chart - NVH: Knock
WARNING: This page is about a different car, the 2013 Ford F-550 Super Duty, 2013 Ford F-450 Super Duty, 2013 Ford F-350 Super Duty, and 2013 Ford F-250 Super Duty. However, it is still accessible from the selected car via links, so may be relevant.
Knock, which can occur on all driving phases, has several causes including damaged teeth or gearset.
A gear tooth damaged on the drive side is a common cause of the knock. This can usually be corrected by grinding the damaged area.