Not sure if anyone cares after this time but...
Got the bike back on Saturday.
As you recall, they had trouble setting up and indexing and noticed the outer front chain ring was out of true.
Anyway they ended up changing the whole front chain set due to it being out of true in the bottom (press fit) bracket.
Turns out the chain ring/s were not out of true, it was the bracket itself.
Anyway, it's all changed now and it rides fine.
They also gave a good lube-ing to the carbon seat post and the seat bracket, resulting in the creaking/faint knocking from that being resolved.
Greased the front wheel hub too.
Whisper quiet and butter smooth now.
I took it a very quick ride up and down the side road next to the shop, so still to test it on a full ride with multiple gear changes, but I am optimistic that all will be well.
I cannot recommend
Swinnerton Cycles (Fenton, Stoke) enough. They have limitless patience and couldn't do enough to resolve the 'issues'.
They're not that local to me (around 40 mins) but well worth the drive for such excellent service.