I have taken the filter back out to re check everything, it is all connected correctly, the rubber pipes appear sound but I did notice the pump wasn't clicked fully home by the 2 plastic tabs.
So I removed the pump to check the rubber gasket underneath, this also proved to be in good condition and have made sure the pump is pushed down properly so that the plastic lugs are in place locking the pump in situ.
Could the fact the pump wasn't fully secure have caused the problem?
I have also replaced the plugs today which I had planned to do anyway as they don't look like they've been changed for a long while. The ones in the bike were Bosch XR7LDC, I have now fitted Bosch XR5DC
Hopefully the loose fuel pump caused the problem and along with some nice plugs and the fact I have the throttle bodies being balanced tomorrow will give me a nice smooth bike ready for my trip to France next week.