As you can imagine, being immobilised for that period of time will have an effect on soft tissue restriction, in addition to the injury itself. The fact that it is now starting to effect your knee may be linked with the mobility of the joint between your tibia and fibula (this need to be able to glide properly in order to function normally).
A problem in this area can also irritate the common peroneal nerve (which wraps around the top of your Fibula) and may explain the referral to your foot.
It may be worthwhile having your physiotherapist look at the mobility of your tib-fib joint, peroneal nerve tension and cuboid bone in your foot.
Let us know how you progress! Good Luck!