Exactly you are doing the wrong training or too much training. You have answered perhaps your own question. Back Off!!. Look for exercises that work on hip extension and stability without excessive patella loading.

Calf raises on the machine are more likely to be training gastrocnemius and you need to work soleus eccentrically not create an overactive gastrocs.

Right now:

Deep Squats: NO
DeadLifts: NO
Lunges: NO
calf raises on machine 3 sets of 8: NO unless working eccentrically with a bent knee
Lots of explosive plyometrics training: NO NO NO

All your exercises are designed to overload the knee joint and all should be stopped right now. Work on stability training on a ball, do more balance work. Do hip 'kick back' type exercises with a machine or resistance tubing of some sort. Whatever you do stop overloading the small hinge joint that is your knee!!!!

Working on the right areas in the right, sports specific way will mean they will do some work in the functional activity and therefore the patellofemoral joint will so less. Hence the training load on that joint will be less. And as this is an over training issue then this is what you need to do. It is NOT weak as a joint, it is OVER WORKED and is behaving normally to being over-worked. Therefore you do not need to 'strengthen it ' specifically. Hope this makes sense to you.