Well I am happy for a short while because I have now done a couple of hundred miles on the Daytona since swapping over the fuel pump assembly, putting the new map on and draining, flushing and refilling the cooling system and I seem to have eradicated the warnings I had been getting.
@Freck Would you happen to know if filling your tank until it can take no more can screw with the Fuel Level sensor? I had an Engine warning twice for the Fuel Level sensor and both times were after filling up right to the top.