It was very tempting to just let this thread die and not come clean but that's not very.....eh.....manly.........!
Here we go, I've continued to struggle to work out what's causing my electrical issues, asking several questions on here. Again, I was checking over the wiring and changing dodgy connections, and decided to have a look at the spark plug. I didn't think the plug was really the source but it was worth a check anyway. I had a visual check of the plug lead and it appeared fine so went to disconnect it, and it clearly wasn't connected to the plug correctly already. I re-seated it (had to manoeuvre the rubber seal a bit), went for a run.......no problems. Took the bike to work yesterday so it was properly warmed up and was in traffic, which is where I normally saw the problem......ran perfectly!
So (touch wood), it looks like that's all it was. Not sure if I've knocked it out (don't think so) or it's been not quite right since I bought the bike. Anyway, I'm much happier now and my confidence in the bike is restored. And today's lesson.......always check the basics........something very simple overlooked can cause lots of confusion!