Heres a novel idea. Maybe you are doing too much gym work, yoga, strengthening exercises, squats, etc. and have put your own muscle balance out. You really do not need all that squatting, gym work, etc. just to move around when there was nothing wrong in the first place.
I'd stop the gym and yoga and get out running again. Or cycling. Don't do squats and lunges - they are horrific for your knees and not worth the risk unless you are an Olympics or Worlds team contender. Avoid exercise which involves changing direction sharply or jumping. You can isolate the VMO muscle and any reasonable PT should have shown you how to do exercises daily which are NON-WEIGHT-BEARING.
I agree with the likelihood of being low on magnesium. Might sound like a strange question, but do you remember your dreams? Do you get cramps in your hands and feet, particularly at night? If the answers are yes and no, it can be a sign of low magnesium. If taking supplements, avoid the basic magnesium oxide type. Or just eat some peanuts or peanut butter.
And stop obsessing and become a bit tougher by moving outdoors more. The amount of detail in your posts and the number of them is a bit over the top for quite a minor injury in a young person. Most of your problems seem to have coincided with doing a lot of gym work and not moving forwards in straight uninterrupted lines, so I'd change that if you want to get better. Or take up a new outdoors sport, such as surfing, to give you something else to think about.