I would do two things see a doctor to look at your knees and knee health over all then i would see a sports medicine specialist to look at what you can do with your bike and as far as training to prolong/promote knee health and third I would go to a shop and get my bike professionally fit to me

In my own experience float in my clipless pedals had caused issues with my lcl and I ended up fixing the problem by going with a zero float pedal system all knees and people are different