OK, so it seems it was my mistake
When I pulled the supercharger I left the injectors/fuel rails on it. My spare stock manifold had all of the original hardware on it. I am not sure of the origins of this manifold, it been in my parts stash for a long time.
I think it mush be very old and the injectors have all gummed up. I swapped the injectors over and now she runs
Something interesting though. The inlet air temp sensor now reads 10degC hotter than before. The harrop air temp sensor must have different scaling to the stock sensor so flashing back to stock is still necessary.