Graham,

Was the misfire there when u had the mot, as if plugs black after a good blast at operating temp, getting the wrong info to ecu, you change the cts, so if fuel pressure correct, and air filter good, then wiring, sensors map, throttle switch,
ats, co% and with the plugs black they will wisk up causing a misfire especially
champion race plugs 57/9's. u say new plugs was it there with old set as i have had new NGK , before for a bike took me ages to suss it as on the block sparking
but after 10, mins of running under compression no spark, so i give them a miss
although some people rate them, i prefer motorcaft,Agpr12pp8's up to 1.6,bar 0.8mm
gap. see what the co is first then go from there what u already suspect,

Dave,