Took the bike to my local dealer for them to check over, and they said that the air filter oil was incorrect, and was gathering in the filter box. They cleaned the filter box and put the correct oil on the filter, and charged me £20.
This has improved the running when hot, but it still takes a while to warm up, maybe I'm just not used to a big single, after riding a Blackbird?
I've ordered some Iridium spark plugs of e-bay, that might help, we'll see.
I still love riding the bike, much more fun that the Blackbird on the route I take, The Blackbird's for touring, not sure how comfy the Freewind would be on a 1500 mile trip up to Scotland.
Thanks for the advice,
Mitch.