if you have a trainer or access to a spin bike, try some one legged drills- they should help you even out your pedal stroke. I find my knees complain most if I am pushing in a higher gear than I should be, or if I am spinning at too lose a resistance, at which point if I am tired I tend to fling my knees around. It helps me to envision my knees driving straight forward ind concentrate on a circular motion with no jerk of pull or push at the top of bottom of the stroke.

as for toes down causing your knee pain, I don't know.

good luck on finding a solution.

marni