It seems quite possibly that I've fixed this problem.
I changed the HT lead and cap from a spare that is currently not being used. This is the only item I have not changed, and immediately it seemed there was a difference.
I was able to get the bike idling at 1200-1300rpm for quite some time (perhaps about 10 minutes), and the charge light didn't come on at all even briefly in the test phase.
Later on tonight I did actually go for a ride and it was successful. There is a second thing to bear in mind though is that the battery I was using tonight is poorly. I knew this, and of course with it being dark and the lights being on the issue of wanting to stall did come up when the indicators were put on. I have another battery which is in better condition to try all this out tomorrow and hopefully fully put this issue to bed. So I think that this is a tertiary issue and not the cause of my problems for me to make this thread. Although at 12.58v after left in the garage with all lights off, the battery reduced to 12.38v within 10 minutes, and I have seen down to 12.15v in the past a day resting after using the bench charger. I will measure the poorly battery tomorrow @ 7pm, and that will be 24hours rest, and we shall see what the voltage is there.
I did some high RPM riding too (5k plus) without the bucking/misfire effect I had a couple of times of late, and all seemed well there too.
Another thing I noticed was that the charge light did not seem to kick in and stay on FULL after starting the bike. So what with that, and the charge light not even illuminating slightly at idle (unless it was sustained) for the 10 mile test, it seems that these were connected.
What I find interesting is the fact that the HT lead that was on the bike I installed not more than 2.5 years ago, and although the outer sheath was slightly compressed in places because of the way it was positioned and the vibration rubbing the lead against parts of the frame, it didn't on the face of it look like a worn, broken or kinked lead. This of course also leads me to the cap itself, which I installed only 2.5 years ago as well.
What would be a most definite resolution to my findings would be to put the HT lead/Cap onto a different bike, and see what happens there- but unfortunately I don't have another working vehicle I could easily test on, except my Trophy. My brother actually needs a new spark plug cap, so I am tempted to give him mine and see whether he has the same issues, unless that is I get my engine rebuild on the ETZ250 done first. I do actually intend to buy a length of new HT lead to implement on the Trophy so might try it on that bike before I put on the new HT lead.
Anyway, long story short- the only electrical item (or pair of, rather) I didn't replace seems like the cause of the issues- but still, I suppose it was good to get stuck into the bike's connections and clean and smarten things up in there.
It wasn't until late in the day when I made the connection between the (rare admittedly) high RPM mis-fire and the idle misfire. My first thought was the electronic ignition but that seems like it is still holding up extremely well.