My knees used to track into the top tube. I adjust my cleat position to optimize where the pressure point is on my foot from pedaling -- this ends up being kind of midpoint of the adjustment range front-to-back and with the cleat as far inside as it will go (Speedplay Zero pedals), but my knees still track up and into the top tube. Varus shims are what my fitter used to straighten my knee tracking.

One of my riding buddies tried to solve a knee tracking issues with Q factor adjustment and had very unsatisfactory results from it -- you might want to try the varus/valgus shims. They are cheap and easy to change out.