I think you're right that I was a bit rough on it breaking it in, Although I still experienced partial engine seizures whilst riding on the back roads in N.Wales.
I took the pistons and the cylinders to a machinist this afternoon. They said it was difficult to tell with the amount of scoring on the pistons but found it to be around the ballpark of 0.003". They too said that the pistons were 'usable' but advised me to get a new pair and to come back for them to remeasure and hone the cylinders to the correct size.
Also removed the sludge trap. An absolute mission but it appeared to be pretty clean inside. I'm not hugely keen to be spending another £100 on a set of pistons though. Then again, these ones do have a decent amount of scoring all the way round and I don't fancy knackering my cylinders (even if the next rebore would entail sleeving the cylinders).
It is also possible that my motorcycle was running too lean and getting too hot I suppose? Then again the pervious machinist was kind enough to join the crankcases together without me asking and without considering the end-float tolerances, so I'm too impressed tbh.
Either way, this seems like peanuts compared to those ignition problems that were plaguing me for months!