Greetings all and many thanks for the suggestions and the questions.
Given the bad sea state I had asked Tim to open the trunks on the way out. I think i said something like " if we really need trunks it is no time to be lookng for them" Sounds prophetic now!!! I am flexible on trunk positioning and respond to the weather conditions. My open trunks do allow water in when the boat is at rest. I also have a Sahara 1100 with a float switch.
I have a water seperator which helps keep the fuel clean. The air vents for the Redbay are in a good position on the console and are of a type that has the breather covered and filtered. I don't think they will let water in but I will check.
Trim: Boat was trimmed very high. We had just completed run approx 8 miles with following sea and no problems. Problem was as we got closer to land the water depth got shallower, waves got steeper, holes got bigger and we did not decrease our speed despite the obvious change in conditions, At times when surfing down the bigger waver we were doing 35 knots +.
Big concern was engine emersion. As ever Yamaha did the business and never faltered despite going under a few times..amazing.
Take it easy ....but, take it all the way.