I spoke too soon.
The issues are still there, admittedly much less severe but still there.
I am going to try and explain what is happening in case anyone recognises the symptoms nad has a cure.
1. A slight hesitation when I roll on the throttle. This is not huge and if I has not ridden the bike 1,000's of miles fo ryears I migh tnot even notice it. However there is a definite lag from twist to go.
2. A severe lack of power when lugging (i know, I know don't lug). That is a little simplistic though. For example going up the hill to my house which I used to do quite happily at 3,000 in second I now need to be at 5,000+ in 1st or the power drops off so badly the bike wants to stall. Even then in the steeper parts I have to slip the clutch to build the revs back up to stop it grinding to a halt on me.
So far I have changed one coil and the HES - I am very open to suggestions as to what to try next...