Update well not so much problem solved but the misfire has at least dissapeared. I set the REVO to standard settings, the wife used it for a bit yesterday.
Today I tried it misfire not there on standard power, so thought give it a whirl with S2 and low and behold- back to normal.
I wonder if the CP could fault intermittendly or whether after connecting the pipe to the turbo the ecu had to readjust to the new correct hardware set up?