I’m not being funny I hope but I have to say yours is the driest looking suspension I’ve ever seen on a Morgan and the nipple shows no sign of having been greased. Perhaps your suspension thumps are due to no grease in the hub bushes.
The cross head has to overcome rotational forces when asked to function in forward motion and if a large force input occurs needing the hub to slide on the pillar that rotational force can cause jamming to the hub movement.
Question, when they upgraded the suspension did they change plllars and bushes?
Did they grease them? They take way more grease than you would expect after a clean and rebuild.
Check for bush wear. Can’t see on your pictures whether or not you have BRB,s fitted, might be a good idea to fit them if not as this will alleviate a lot of the rotational forces at the cross head on breaking or when the suspension is asked to respond instantly and with a large compressive force. Lastly, on a newly rebuilt suspension I really would expect to see a lot of grease blobs splattered around as the excess is ejected under normal use, again I can’t see that indicating no grease to expel so I’d start with assessing bush wear and grease level first.