Today i got my bike back from the dealer, one week earlier than he predicted - i'm impressed. You couldn't tell they had taken her apart expect for the copper grease lube on the rear engine bolts - a really nice job.
What they did:
> Remove engine, remove lower crankcase halve, remove gearbox main and lay shafts
> Fit new fifth gear on main and lay shaft
> Rebuild and refit engine
What they found:
> Visual inspection only between old and new parts showed difference in machining marks on the old fifth gear part (only one of them but they could not tell me if it was the main or lay shaft gear - already sent back to Yamaha UK). Essentially they observed unexpected marks on one of the old fifth gears and confirmed the replacement part did not have the marks. (Sorry - i could not get any photos, i can understand their reluctance)
Result:
> Dealership owner rode my bike 'before', rode a 'Yamaha UK bike' and rode my bike 'after', he reports no noise now present in fith gear and bike sounds just like the 'Yamaha UK' bike he borrowed.
> I've ridden the bike only a few miles so far, again no sign of the whine, i'll put some more miles on tomorrow hopefully to check it out a bit more.
So in summary, i'm glad i had it checked out, it seems to be fixed, the dealer was excellent, and i'll keep you posted after a few more miles on the new gears.