Strange so there is no area to fit a bilge pump towards the back of the boat? it is all a flat floor all the way? Any pics?
Two things to check for leaks, make sure your bungs are sealed properly, like the little rubber grommet around the bung is in good condition.
Second, not sure how the wiring boot is from the engine to the back of the boat. I know in some boats it is open and water comes in - but then again you would see this if you didn't have a floor all the way to the back.
Third thing, now that you have removed your carpet, check all the joins around your boat, so when you wash it down, water is not flowing in from your hose. There was a member here with a Tournament and was leaking water from the bungs. All that time it was coming from when he was washing his boat out.