It's difficult for you to judge how your foot is hitting the surface when your on a run. Plenty of running shops video your running action in-store and supply footwear that corrects pronation issues. Avoid the £20 bargain stores and pay a bit extra for some specialist help.
I've strained knee ligaments on a couple of occasions and all was well after 6-9 weeks. Depends on the severity of the strain and your activity levels during the recovery period. Put your feet up and rest - that's the best cure.