Id try moving the cleat on your shoe to the inside or outside and see if that relievs and pressure on your knee. keep in mind that cycling can add stress to your joints and ligaments. I just did a 90 mile ride yesterday and by the last 10 miles or so the ligament behind my knee was hurting a bit with each rotation. just a matter of conditioning.

as far as your knees almost brushing your top tube. thats good form. maybe not having any degree for your feet to play with is putting strain on your knees. If you had even a 5 degree for your foot to play with.