I know its been an age now, but thought I would just give the conclusion to this problem. I took the bike to Rich Llewellin at Louigi Moto, as soon a I described the problem he came up with an answer. Which was the ECU needs remapping. He did this for me and the bike now runs like a dream, I have put 6000 miles on it since the problem and it hasn't missed a beat, much smoother too, starts first turn every time and has never cut out since.
