[willy]

Nice set up, fisherman involved for sure. Is is around an 1983?
As far as the water coming in thru the scupper drain holes some guys have put one way valves in the lines between the scupper and where it goes out thru the hull.
I remember mixed results with that, mainly due to fish and general boat crap fouling them up.
Her is what I did on my 1986 which had the same set up as yours, and even though it sat just slightly higher water line to scupper thru hull I still got the same thing when bobbing and weaving on the drift with people in the back of the boat. I took two of the garber type plugs that are rubber with the fold down toggle to tighten them and put one in each corner when I was out fishing. No more water problem, never interfered with anything and bone dry.
A word of caution though, you MUST remember to take them out when you tie up at the dock, or get put on a rack or whatever, at the end of the day pull them both and stick them in the corner drop down box. Otherwise you will have a giant bath tub with rain etc. and could sink you boat.
Second MUST is this, if you are out on the water and the rain or waves turn to sh!t pull the plugs and put them away, they will drain your boat fast for you, especially at speed on the water and are an important safety thing when life throws you that once in a blue moon curve to deal with.