So as
@Sano said knee pain is complex. My new found freedom to squat led me to smolov, it was glorious and squats are forever changed for me, but I failed to do the relevent stretching.
I went for a tryout day to see what I could do now athletically without ramping up to it and I really felt the lack of prep. Knees hated sprinting etc, shooting pains in lower back. I performed reasonably but didn't really recover for the best part of the week.
All the squatting obviously put extra pressure on the already tight structures at the top of the quad. So I started stretching it out and over the next couple of weeks have reduced the recovery from 4 days to 2. Also started using instep inserts etc.
Went to a physio to keep the momentum going and she decided the problems lie in the hip, at least that's where were looking. Peraformis stretch, hip flexor stretch, advanced clam glute medius exercise trying to activate glute more, several times a day. Also I'm foam rolling the muscles that attach to the IT band at the top of the leg.
Squatting and bending knee is still a pain free activity but now we're trying to make the knees not flair up with petaphemoral pain after athletic stuff. It's pretty exciting being able to fix stuff this way, I can't believe I'm going into my 8th season, old and yet strongest I've been, coach wants to try me at full back if we recruit well enough to the o line, not sure my head can handle that and we won't recruit enough but it's a testament to the improved mobility.