Right ok took it to a garage that had a lift, it would seem that my spring has spun round so wasn't located into the top cap stop end correctly which is what was causing the clunk. Spun the spring round and it isn't clunking anymore, will keep an eye on it.
I have Eibach springs that are ever so slightly shorter than standard, but I definitely bolted them up correctly to the new shocks, so they must have spun round at some point whilst the car was jacked up with the weight of the suspension and wheels extended the shock.