Just to update myself and anyone bored enough to read my posts here's where we are to date.
Looks scary to me but some of you spanner warriors would probably relish the challenge.
After all the horror stories of balance shaft problems I decided that I should check it out, rather safe than sorry. I'm happy to say that the woodruff key and shaft are as Mr. Yamaha intended. I have retorqued the nut and fitted a new tab washer so hopefully that's that.
So far the worst thing I have found is a timing chain I suspect of being very worn. I took the spring out of the tensioner and then removed it. I estimate that the plunger is out by 65-70% of it's range of travel so I've decided to change the chain. I did notice the sound that the guide blade made as it flapped around and it's very familiar. Is it possible that this was the clacking I heard and the chain was so worn as to throw the static timing out slightly?
I turned the engine back and forth a degree or two and there was a very slight clunk from somewhere around the bore. The barrel came off for a look but I can't feel any vertical movement on the conrod, just a slight clunk as the piston moves side to side on its bearing. Should this worry me or is it normal?
If you turn the volume up you may be able to hear what I mean:
http://youtu.be/y15rFw7N9u0
So, with the inspiration born of blissful ignorance and financial desperation, I intend to put her back together this weekend. From those of you who worship the Lord I would appreciate a prayer: from those of you who worship Mamon I would appreciate your spare change.
Thanks for reading.