Finally got the car back last week after just over 3 long weeks of it being worked on at Krazy Horse. It was very frustrating at times but I tried not let to get to me as I knew it would get fixed. In the end the EU4 ecu was causing all the problems. Once that was replaced the car has been amazing and not missed a beat. Well a relay did fail today, fortunately I was next door to a mechanic and various calls back and forth with Krazy Horse the problem was sorted.
I 'm learning a lot about this car which is a good thing and I'm sure in time it will become very handy.
Once the EU3 ecu was on the car Dan, the mechanic at KH, said the car was producing more mid range torque and power which make the car a bit more fun.
So for anyone with an EU4 car experiencing problems with doing a stage upgrade it may be the ecu itself that is at the heart of the problem.

