I finally sorted my misfire (I think)!
Tried a new ignition coil as the symptoms pointed that way. Still had the issue. Removed the PCV, issue gone. Last night i refitted the PCV, issue returned once bike got hot.
Now I couldn't get my head round why a fuel controller only misbehaves when the bike is hot. The PCV connection to the coil I hadn't cable tied to the frame, I'd let it hang about half way between the frame and the rocker cover. I cable tied this higher to the frame. A short ride and the issue seems to have gone, by this point it was very dark and freezing outside so the test was short. It'll need a much longer test ride to be sure but it seems when the connection between PCV and coil was getting very hot it was disrupting the coil and giving the symptoms of a coil breaking down when hot.
I hope I'm right, I can't think why otherwise a PCV would go haywire only when the bike is hot.