It turns out that we were several little issues that made the forks harsh.
1. A little light on fluid - needed a change anyway.
2. The bumpers were in there, from the last time I was in there, but Tony put a new set in, as he had them.
3. There were some preload spacers I put in from its café racers days which are no longer required. Those coupled with firmer springs made the forks too stiff for a Bobber. This was not an issue when this bike was a café racer, as the clip-ons and rear sets put more weight up front, but when the weight moved back, with a more upright riding position, the forks would rebound with a 'clunk'.
As was the tuning, next time Tony messes with his dynamic timing he want to sung up the bolts of the bean can and points a bit more, then they wont move. The bike is now as fast as it ever was. As I can testify as I was overtaken by him on a spirited ride over the Wiltshire downs a week or so ago.