Well, I lifted the tank and checked the wireing and connector, all looked fine so it sprayed some WD40 into the knock sensor and connector block. The light had stopped flashing but was on constantly. While it was running I could hear a rattle coming from the can. When I looked inside I could see the flap was in the open position so it looked like I had connected the cable to the servo incorrectly (it wasn't connected when I got the bike) I ended up rotating the servo 360 degrees and reconnecting so the flap was in the closed position Started it up again and the light came back on after a few seconds, I don't know why I did this but I turned the ignition on and off six times and hey presto all is well on the dash again I even started it before I left for work this morning and let it run for 10 minutes and all is still well.
The EGCA (Hondas name for exhaust valve system) fault code would flash 3 long 5 short to inform of on issue with that.