I think the reason the legs ekep looking off is because you've not put any light on the knees, even though those stick out and should receive light along with the upper leg. As a result, I think you've confused yourself about the lengths of the upper and lower parts of the leg, making the upper leg too long.
Here's a possible fix:
I put light on the knees (including some on the sock so it doesn't read so much like a shadow), and shortened the upper legs by 2px. I also made her thick a bit thicker, because she had weirdly skinny legs (even in the ref she has some thigh flesh).
Even with my fixes, the boots have some lighting issues. Try to shade the calves as if they're simple cylinders, ignore the fact that they're boots. As-is, it looks like you shaded the boots as separate objects without taking into account that they're just part of the leg. They seem to have shading at the tops of them, for example. Why would they?
Also her hair's lit from a different direction than her torso xP
If what I said here doesn't make sense, just say the word and I'll do an edit.