Thanks for all the feedback and suggestions guys, much appreciated.
Hopefully these images help clarify.
Here you can see the whole cockpit from the stern
Here from the cabin
Here you can see I have installed my imperfect solution. 2 external holes in the transom, they could have been maybe 1cm lower but that would not have made a major difference.
Here are the internal holes which are approx. a diameter higher than the externals to create a fall, all this assumes I got my levels correct as we have not had the boats on the water yet.
Here is the internal crossover pipework.
And here you can see the step up into the cabin. I filled the cockpit with water and the current arrangement makes sure the water level is 1-2cm below the lip of this step. However just to be sure we prevent water getting in the cabin we intend to split the washboard with a small 6 inch section at the bottom, this will be fixed in place and silicone in position.
So the heel or floor of the cockpit is definitely below the external waterline. I think we will be safe when moored with this current system but when sailing are we only left with a mechanical/ pump solution to get rid of this considerable weight of water????