My dual pumps aren't perfect in their calibration, but it is something that I can live with, however I put a john guest valve and I must have increased the pressure on the pump tube and it wore a vertical groove into it. The pump came with replacements, but fair warning. The other is holding up fine with the same amount of wear.
A valve of any sort on a peristaltic pump won't be efficient, especially on a dual headed pump such as the Stenner. Since it's driven by one motor, the valve will essentially transfer that resistance to the motor, thus slowing the flow on both lines. Also, if you put the valve on the suction side, it'll cause damage to the lines of the pump. One way of fixing your calibration could be to decrease the hose size on the lower pumping head. Never tried it and would be a small investment to figure it out.