Ive got a "Y" Reg FZS600s, had the very same problem years ago, was advised changing the selector forks and shafts would sort it. which I did. Never took the engine out though. I removed the tank and fairing, drained the coolent and oils, got a thin-ish matteress off a zed-bed thing and layed the bike down, clutch side up. Removed the clutch casing, Clutch and sump (IIRC 2 of the 5mm allen head bolts were awkward to get to, but boom, she was off. It solved the problem momentarily (500/600 miles-ish) but the problem soon returned.
Later, after obtaining and fitting a 2nd hand engine, I spoke to deefer, who said I did right but I should have changed the selector drum as well!!! Will know for next time eh!!
but as daunting as it looks at first glance, its an easy enough job as long as you have a half decent set of tool's and ALL the replacement parts (Drum, selectors, shafts, gaskets, oil and oil filter and just to be safe some black silicone gasket stuff) and a good few hours un-interupted (if your a novice/intermediate skill level) take your time, take pictures if need be, and you will be fine. Id do mine again without a 2nd thought.