Its very difficult to diagnose remotely - and sometimes having the box in bits doesn't help either.
I have just rebuilt a box for a member in Ireland. It was sent to me because it was leaking oil from the output shaft rear oil seal and he couldn't get the drive flange off.
I said I might as well strip it while I had it and check it over. . . . . .
The front bearing on the output shaft had partially collapsed, the cage was in bits which were lying in the box and the balls were grouped at the bottom of the outer track. The oil baffle in front of the forward bearing was chewed-up. Two other bearings were shot and the box was full of swarf.
I cleaned it out, machined a circlip grove in the output shaft, put all new bearings in, new seals and springs and it seemed fine to me - smooth to turn and the gearchange was good.
Later it was sent back to me as it was
"noisy - and it didn't do that before" 
.
I went right through it again, set the shafts between centres and tested them with a dial gauge - all ok, just minimal run-out (0.07mm max).
I took the centre out of an old clutch plate, turned it up and mounted the box on my lathe - it ran nice and quietly with the gearchange just clicking into gear. I gave it half an hour, changed the oil and gave it another half an hour - all fine. What I can't do, of course, is mimic the power pulses of a ticking-over airhead on my lathe, and I drew the line at fitting it into my bike and trying it out (though I now wish I had).
It has now gone back, but I expect it will sound the same when fitted. I suppose it could be excess clearance between the gear teeth after its initial trauma but unless I replace everything in there on the off-chance of finding the cause there is nothing else I can do.
I have received a video clip of the original noise - with the bike ticking over there is a definite clatter that is quieter when the clutch is pulled in - is it the box or is it the clutch ??? I can't tell from here.
The reason I'm recounting this tale is that it is very difficult to pin these things down. A 'klunk' on initial blipping of the throttle could be a very worn bearing or possibly the shock absorber if the spring is weak and/or the cams worn.
Swarf in a box is not uncommon and doesn't necessarily herald imminent failure, worth investigating if there is a lot of it though.
If it is a worn bearing or shock absorber I would expect you to notice a klunk when riding the bike and going on and off the throttle - is there anything like that happening ??
How old is the clutch friction plate - could the splines be worn ??
If you are going to worry about it I would remove the box and get it overhauled (I'm not looking for work - I have a Toyota Landcruiser Transfer Box in bits on the bench and you wouldn't believe the state of that, Its going to take me a while to clean it out let alone fix it
).
Peace of mind is worth a lot when you're a long way from home on a wet night relying on the bike to get you back safely
.
I hope you track down the noise/problem. Please let us know what you find.
Bob.
)
