That's about right the brake pedal is higher than the clutch just like you described ..why....they wanted to take three inches off but you cut two with no ill effect. The lad has tremendous push strength in his leg his birth defect is the knee and having to lift it at such a weird and high angle it's tuff it's just not lift but it's moving your leg at an angle and lifting from the gas pedal. Perhaps we could start at two inches see what happens. Your fix sounds just right line up clutch and brake pedal for smooth movement. We all need help sometime....