Thanks for the update kasapoff, it is was a guess on my part but looks like I now know what needs doing. Thanks again for all the thread updates.

kasapoff wrote:

Finally resolved - as suggested by Alex and Thrud, it was the EGR. Mapped it out at an indy shop few days ago, so far happy with the outcome. No more dreaded hesitation, better throttle response at low rpms, overall tighter feel of the engine. Good luck to anyone with similar symptoms, hope this helps.

In my case it involved updating the engine settings, yes. If you take a small video, I can confirm if the problem is with the EGR. There are some clear patterns.