Told to quit squatting movements

Over the last 2 years I've had a number of injuries from the High Intensity Training i do (CrossFit- strength and conditioning programme). I think my injuries and treatments have been symptom focused and and deeper issues haven't always been addressed. I've not had anyone look at what I'm doing in the gym and what stresses I'm being put under.

At present I manage these conditions. I'll number them in terms of the order they appeared:
1) Tighter left hamstring than the right (had since pre crossfit from football years)
2)Tight hip flexor especially left side (stiff when get up from sitting long periods at work)
3) Shoulder impingement during overhead lifitng
Tightness in the left hip/pelvis hip which gets relieved when I stretch laterally to the right.
4) Tighter IT band in left leg than right (managed now with foam rolling, ball massage).
5) Significant number of tight spots in the left quad
6) Dormant left glute (This was highlighted as not firing well but no one addressed it as a major problem until recently as knee pain persisted. Knee valgus identified in left knee led to glute activation work. I personally believe this is where my knee pain stems from after research I've done)
7) Pain in quad tendon first just above the knee- patella found to be stiff and pulling upwards. Then further pain after burpee exercise over the kneecap creaking inside the knee identified as wear and tear of cartilage starting due to tracking issue (patellofemoral/chondormalacia???). Quad flexed stretching became painful
5) Poor muscle development/mass in left Vatus Medialis Oblique

The physio who last saw me was a Sports Injury specific clinic ruled out them being linked or systemic and he thought I was too fixated on my injuries and basically just told me to avoid what was painful..essentially quitting squatting movements/ kneeling down. That was heartbreaking to me as a major part of Crossfit is olympic weightlifting and multiple varied squatting movements. He had no interest in analysing my mechanics to see if corrections could be made before then seeing if the knee pain persists. I only want to stop those movements if I have exhausted all possibilities. So I am looking for other opinions. I am working on my glute activation and have pulled of a programme from an online hamstring dominance article.

I've been advised to work on straight leg quad exercises which I am doing. I've decided to start supplenmenting with glucosamine and possibly chondroitin for the cartilage management. I want to correct all mechanics, return to squatting which i have not done loaded for 8+ months. If the back of the kneecap is no longer smooth, can that be explored to see the damage extent and shaved with surgery to prolong my training? My prime concern is being able to demo exercises and I hope to teach crossfit one day.
Is it unrealistic unless you are a professional sportsman for your mechanics, and sport specific activities to be analysed as I have failed to have this done yet by anyone I've seen?