Oh, another tip; learn to read your knees.
Did you have any sense your knee was upset prior to this realisation? Probably. Did you think it would go away? I have in the past. But you have to spot the way things are going and adjust your approach.
As
@vickster said, Welly in the wrong position will chew them up. You might be really happy you found the right geometry, but definitely play around because your knees might disagree with you.
Height, how far forward the saddle is and so on... Easy to adjust, hard to get right.
Edit: oh and I am sorry to hear about this. I share your pain.