Agreed. The floats do appear to be rigged a little "flat". However, shortening the rear strut will increase the in flight drag a bit, particularly with your wide floats, thus slowing the cruise speed and possibly reducing the climb rate. How much, I can't say. My recommendation would be to try changing the flap setting first before altering the struts. A good flap setting for take off would be to set them to match the deflection of the aileron when it is full down. Or in other words somewhere in the 20 to 25 degree area.
I did two new rear legs 1 a inch shorter and 2 new bolted fitting half a inch longer. So I can try half a inch or a inch shorter. Just have to make my mind it is all worth taking the time to try....
Also, in rough water more flaps will help in reducing pounding by increasing the relative AOA to the water surface thereby lifting you out of the chop faster. Then accelerate in the "water effect" (AKA ground effect).
Myself, I would try 20-25 of flaps before you switch rear struts.
Did again follow your advices. I've putted the plane on floats this week with the same rigging. With a little more flap, the takeoff are perfect for me. Maybe the VG's and the flying time helped a little.