Same issues here with my left side from my elbow, to hip to the knee. Im pretty sure its from an imbalance and the knee and hip is definitely from the glutes not firing properly. Its hard for me to get in the rehab along with training while working 55hrs a week so its motivational to watch u ;)
Yeah I had been having knee problems myself. You should also check out Dr. Aaron Horschig from Squat University. He has some great stuff and I know he works with elite athletes such as yourself.
I have the same hip issue and notice it takes a while for me to warm up and get comfortable to perform the heavy lifts. How often are you doing these lunges and movements? Everyday?