Patella on outer sides of knee

Hello there!
I do like your opinion and advice on a case, but first I will provide some background information.
I’ve been lifting weight since I was 15, with occasional jogging. Demotivated because of my injury, I quit when I was 19. Now, I recently started some jogging in vibram fivefingers 1-2 times a week.

I’m 22 years now, I don’t have precise data, but I believe around end 16 the pain started in my left knee. The cartilage behind my kneecap got irritated (I believe it is called Patella Femoral Syndrome and Chrondamalacia Pattelae). I’ve had several years physiotherapy (different therapists) without results, including an x-ray and MRI scan and a visit to an orthopedic specialist. Then another scan and x-ray and some other specialists. The same diagnostic was made, but a different treatment started: ARP training (this is with an electronic device, connected to my knee).Exercises where mostly the same, (with the same emphasis on my VMO) I was also giving soles by a (sport)podiatrist, because while running my knees slided a little to the inside and I was superpronating. After about a half year we stopped and it seemed to be a success.
However the pain returned some time later (approx. a half year later?). I discovered the barefoot/minimal trend, and the whole philosophy seeming logical to me, I switched my Nike Air Max shoes for Vivo Barefoots. This was two years ago. About two months later, there was a significant difference. I was almost having no pain in daily life. I still don’t, with some exceptions (with prolonged sitting on a chair for example). Nowadays I’m almost only wearing minimalist shoes (again, with some exceptions) and a regular shoe just feels bad. I abandoned the soles with the shoes. I almost don’t pronate anymore, and my left feet, from which the toes were a bit deformed, are getting more straight with time.

However, my knees, especially my left one, doesn’t feel really ‘stable’. I’m almost certain that when I put much weight on it again, pain will return. And unlike the past, when as a child, I was able to sit a lot on my knees, I can’t do that today. When bending my legs, my patella is placed on the outer sides of my knees, see the photo’s (both knees). Sitting on them (unless at a soft material) just hurts. Why? They haven’t always been like this. Is there a way I can straighten them again? How?

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First of all thanks for reading, I hope you can point me in the right direction!
Of course I can also visit some local physiotherapists (again), but my past experiences with them (I’ve also had other injuries) are not really positive.