Good news on the running front. Weirdly, after changing the original plugs for hotter versions (7ES) and it running better, but still intermittently as if on limp mode, I put cooler ones back in (8ES both NGK) and it ran terribly. I've been a bit concerned about fake plugs and read about Denso versions being less likely to be counterfeit and also having a stronger spark. So, I thought it would be worth a try.
Anyway, I fitted them and it immediately ran as it should. Not perfect, and a bit lumpy, but strong and powerful and not as if on limp mode.
I've never had a bike that's quite so sensitive to spark plugs! So, for now she's ride-able, albeit a bit clunky on the gear change, especially on engaging first from neutral. I suspect this could be a common trait though. Thanks all for you help so far.