Sounds simple, but I’d be checking the connections/lug faces on your isolator and battery.. If you lose battery power intermittently you are running off charging voltage only - which may not be enough to run fuel pumps, etc.. I have seen this before. Isolators are generally in a position where they can cop salt, etc.. worth a look anyway.. An indicator might be that your charging voltage is slightly down on dash. Personally, I’d solder the cables into the lugs, rather than crimp. 

Hope this helps 

 Clasic sign of the fuel tank vent not working correctly.  Getting a vapour lock intermitantly.  Run it off a portable tank to see if it is the problem.

I doubt this is the answer, but had a similar issue on my old tinnie with a 2 banger.

The fuel was stale and had formed a jelly substance in the fuel bowl of the carby.

Was fine when flat, but trying to get up on the plane the jelly would move in the bowl as the boat was on a bigger angle and would close off the float and the engine would get no fuel.

It's the intermittent faults that are always the hardest to diagnose.

Good luck.

You say that with a following sea, and coming down into the trough on big sea it appears that the motor drops revs.

Could this be caused by coming down into the trough the motor/boat is actually surfing to some degree, if so you will notice that the motor increases revs as the amount of energy to push the boat is greatly reduced, hence engine is not working as hard revs increase.

When coming out of trough engine has to work harder and revs will decree.

You can check this out very easy watch the tacko when coming down a wave a in a following sea ( not a big wave you shouldn't surf down any wave if you can help it) you will see via tacko increase in revs when you are in trough revs will decrees as the motor gets the increased load again.

Just a thought outside the motor box

 Hi all who are interested.

i checked everything and serviced everything and still had the motor cutting out at the bottom of the trough, both going into the wave and coming over the back of the wave and hitting the trough. i finally found a mechanic that was willing to chat about the issue. he told me before he would bother coming to have a look to change anything that i had 'modified'. The only modifications i had made was changing the prop in an effort to gain higher top end speed. I started out with a 17 pitch and changed it to 19. This gave me about 6 knots more speed at all stages through the rev range. I then put a 23 pitch which gave me another 3-4 knota top end and cruising. (Preamble over).

After speaking to him I changed the prop back to the 19 pitch. I tentativley took it out in calm weather and had no issues. I then took it out during the last storm with huge seas and again had no issues. My latest test was in relatively calm seas but with a reasonable swell and had no issues. 

My theory is: with the high pitch prop the engine was maxing out on the torque. I was not able to achieve max (WOT) revs. Then as I hit a bit more load (at the bottom of the wave or the trough) it overloaded the torque on the motor. Sort of like when the prop is wrapped in rope it just stalls. 

 You must of be lugging that motor trying to turn a 23.  It's a must to be in the optimum RPM range at WOT carrying your normal load. Something that gets overlooked for top end speed.

 Top speed isn't everything. Boats don't have multiple gear ratios to work off, and that prop has to do it at all speeds. Going from a 19 to a 23 is a massive increase, unless it was extremely underpropped to start.