Quick update on this one.
Found water and corrosion in one of the ECM connectors. This was bad enough to corrode two of the pins completely off. A little bit of crafty soldering and I have brought two wires out of the ECM to connect to the existing loom. So the engine now runs ok. The problem I now have is working how the water got in there in the first place, it is extremely unlikely it has just dripped in. I think it is likely that one of the sensors (CTS or lambda sensor perhaps) is leaking and forcing contamination up the wire, if I don't find and fix it it will only happen again!