Without wanting to push you for more answers, you say it quits when you use the clutch. As in you are still moving, coasting if you like. And in top the rattle is gone?
Could you have just not been traveling fast enough and it was the engine pinking and protesting at the load rather than any mechanical problem in the box? Just an option to consider, especially as pinking does sound like a little pebble shaken in a tin can.
Its just with the noise only happening in top when the clutch is engaged makes the box unlikely. If it was a problem in the box it would be there from whichever direction its driven. Its just that the gears on a motorcycle are on 2 common shafts, so any rattles generally affect all the gears as they share the same bearings/shafts.
As i said i know the tidlers boxes well enough but i've never played with a FZ, but thats my feeling at the minute.