Well after too long with work getting in the way of sorting out my boat, I managed to do the tests suggested. All resistance tests checked out ok on the stator, coils, etc. This indicated that it was probably the CDI. I replaced the CDI and I've now done two runs of about 10 miles each and it sounds like a new engine, quiet and looks to be a bit more fuel efficient. Sea state has been a bit lumpy to really open her up but its more responsive than before.
I think I've been running round with a failing CDI for some time for it make such a change to the engine.
I hope this helps anyone else with a similar problem
thanks for your help all,