Thanks for all the advise, suggestions and feedback on your own engines. Useful to know that other oversize engines do not appear to have the same problem.
After a bit more running in, I've felt happier to rev it a bit higher and with that, the vibration seems to have lessened somewhat. Still something there but more of a buzz now. Although finding the not fully tightened bolt on the torsion bar arm has probably made the most difference. In time, I will probably replace the torsion arms rubber bushes for new.
Unfortunately, one of the windows on the carbs is too fogged to see the white dot on the slide, so I usually use the "lollipop" method (albeit with plastic glue spreaders instead) to balance the carbs.
However, I decided I would give the carb balance one more check this evening, so stripped the tank and airbox off again. This time, I went by checking the bottom of the slide against the top of the carb opening with the throttle nearly fully open. It took about quarter of a turn on one adjuster to bring them both to exactly the same level and I can't imagine getting them any closer balanced than this. So, I'll give it another ride tomorrow and see if there's a difference.
Annoyingly with the tank off, I noticed that the coolant level in the expansion tank has continued to drop (I posted previously about this) and I can't imagine it's still trapped air escaping any more. I'll see where the level is after a couple more rides, but if it keeps dropping, it looks like engine out again. There are no external sign of leaks.