If knees over toes hurts the knees, it sounds like your quads are tight and not moving correctly and more than likely have some deep adhesions (usually in the outer quad) as the root cause. If the quads cannot stretch, the knee is not supported and the quad feels like it is not working. I use a lacrosse ball and acumobility ball against a hard wall (not drywall) to explore, find and get rid of adhesions in the quads. Regular rolling does not expose these very well and certainly does not get deep enough (and isolated enough) to get them to release. Again, more often than not the ones that cause the most problems are found in the outer quad. Hamstrings cannot contract well when the quad is tight and vice versa. Just one good adhesion on one side can completely derail squatting for as long as the adhesion remains and then we just get further and further out of a healthy squat pattern. I also use a PVC pipe for rolling deeper stuff instead of a regular roller. I am a 56 yr old powerlifter.
Just want to second all of this.
Muscles will hurt and be weak where they are not comfortable and used to moving, and they’re not going to want to move into advanced ranges even unloaded if they’re being restricted by scar tissue/adhesions.
You wouldn’t believe the stuff that has been worked out of my bicep, forearm, tricep, lat insert, shoulder capsules, and pec by my ART guy since I had my elbow scoped over a year ago. I am just now starting to get my shoulder on that side moving more how it’s supposed to.
Until you remove the adhesions and get it loosened up, you cannot move properly.
I would not stop the hamstring work - this lends stability to the knee. You just need to be able to get to where you can begin pushing quad engagement as well and then restore that tissue tolerance in more range of motion as they strengthen.