Hi all, thanks for the great replies.
I have used the classic engineering approach of going for a walk and then a beer to think through the problem.
The alternator was working well. Since then I have reduced the pulley size and also put new cutless bearings on the drive shaft.
This has led me to think the following:
Rather than the diodes breaking down on regulation, I may have been stalling the prop shaft in the quest for more power.
If the battery bank is reasonably full, then the load on the alternator is small.
However if the batteries are low, and the boatspeed high the alternator is creating too much torque, slowing the shaft, and cycling like that. Too much torque, stall, build up speed, repeat
This is exacerbated by surfing down a wave, (fast) then slowing at bottom of trough stalling shaft at same time, almost like a double whammy.
In the interim, I have gone back to original pulley giving me a ratio of 4.8 to 1 (down from 6.9:1)
This has the effect of de-rating the power of the alternator and hopefully not stalling the shaft.
This idea came from a great blog on the subject
http://lifepart2.info/equipment/prop-shaft-driven-alternator
I've got to do the remainder of the calculations for my setup but I am slightly hopeful!
I also probably will redo wiring to the battery bank over the winter, and install a sense wire to the house bank.
Many thanks for the ideas and suggestions. If money was no problem I would modify a manual jabsco pump, coupled to a pma with external regulator, however there are other more pressing improvements on Emerald of a higher priority!
I will report back on the success of the de-powering. The alternator should still provide a useful 5-8amps at our cruising speed.
Once again thanks for all the input and ideas. What a great forum!