So I've put the valve covers back on and tried to start her up.......
....and she sounds beautiful
The first two or three seconds sounded a bit noisey (almost like something was "tightening up") but then she sounded the same as ever. So no issues re: valves/pistons having lunch and started first pop :)
Well chuffed and thanks to all for words of advice and Will for offering to pop over this morning (had to cancel since I forgot about a kids birthday party my daughter wanted to go to). Been home for a few hours now and been non-stop working on the bike! Wifey wasn't too impressed but hey, there we go lol
So valves checked... few just on tolerance but I'll check again in 9k miles unless I have any reason to suspect something is up. The front cover was a bitch to remove but once you've worked out how its done its just time consuming.
I've also cleaned and re-gapped my iridium plugs (although 3 of 4 didn't need it) cleaned/added new electrical tape on various cables and generally tidied things up. I also gave the throttle bodies a good clean, greased the springs on the throttle mechanism and serviced the pipercross air filer using the K&N cleaning kit (thanks to Alad for recommending that some time go). The heat shield on the inner side of the tank that protects it from the rear cylinder was peeling and pretty grotty so I replaced it with some heatshield I had for some panniers a year or so ago.
I'm just about to add some window sealant around where the filter joins the carbon plate of my Rene kit... there is a very small gap at the front I never noticed before and I read somewhere on here (think it was paddy) who added some sealant. Anything to reduce the possibility of crap being sucked in there!
All thats remaining engine-wise is oil, filter and balancing throttle bodies.
Here's a couple of pics:

"There is a grey blur, and a green blur. I try to stay on the grey one..." - Joey Dunlop. Isle of Man TT Champion.