Hi all,
I just wanted to say thank you for all the encouraging (and even the less encouraging) support.
Paul W's note gave me the optimism to pull it all apart again. I was expecting that I'd done something daft like put the piston in wrong, but no - it was fine.
In the end I don't know what the problem was, but its working fine now and sounds great. I'd say the compression is more than I had before and maybe that was what I was worried about, maybe it was hydraulic locked, maybe it was all just over-cautiousness on my part, I'll never know.
I'm not a complete novice when it comes to car mechanics and have good quality tools, but I'm not overly well versed on motorbikes and especially 2-strokes, so this was all new to me and I've learnt a great deal from the experience.
I accept that diagnosis over the internet is impossible (I should know - I'm in IT), I really just wanted some ideas before going to the stealers as I'd already spent a great deal on parts.
Thank you all once again and all the best for your season's riding.