Havnt checked that i will have a look and report back. Thanks again folks for the help really appreciate it :)
I have it booked in tomorrow need to get it to the garage tho still need to figure that out. I have breakdown cover so i might call them up.
I will report back tomorrow.

Update
 

Got the bike looked over today at the yamaha dealership. They have checked the gearbox and its fine. There has been no obvious damage from running it low on oil.

However the couldn't find what was causing the noise. They think it might possibly be the bearings in the rear wheel and sprocket carrier hub are heating up and causing the the noise as the seals were gone and but they still feel not to bad. They are still not sure what it is.

While they were swapping the hub bearing out the hub cracked really badly. Looks like the previous owner had a chain snap and its seriously damaged the hub. It was badly scared on the outside of the hub and when the mechanic removed the bearing the hub basically split right down where the bearing sits. Looks like it must have had a fracture from when the chain snapped on the previous owner. They have gave me a courtesy bike so i can get to work. Will report back after the hub is replaced and new bearings fitted.

Should have the parts in by next weekend so will be report back then.

ouch..are they accepting liability on the hub?..

Nope but its not there fault the hub was badly chewed up from the chain snapping with the previous owner. Plus i watched the mechanic when it happened he wasnt to hard on it and it just gave up. �200 fitted with all new bearings, bolts and nuts. That includes labour and all the parts i thought that was ok. Still not 100% sure thats what was causing the noise but im sure its not helping. Plus got a courtesy bike free of charge which I really cant complain about.

Fair enough..i guess its a lot better than the hub going when your riding it!

dont bear thinking about.

Yeah that was my exact thought when i seen it brake on the bench. Hopefully getting it replaced with new bearings will sort out the noise.

Glad your bikes getting sorted ...hopefully this will cure the clanking. Steve

The rubbers chew into the metal, I'm afraid that the sound has not gone away, hope it's not in the gearbox, still hear it when applying power, from 2 nd to top, quite worried
But, can it be the chain slider on the swingarm that's gone?

https://c8.staticflickr.com/9/8280/3...74a90b96_b.jpg

https://c8.staticflickr.com/9/8560/3...99b83249_b.jpg

https://c8.staticflickr.com/9/8408/3...b164dd87_b.jpg

Seems this is a weak point on the XT660Z ?

Mines was not as worn down as yours mate. The mechanic still isnt to sure whats making the noise. My bike should be back on the road by this Friday. Mines mainly makes the noise when the bike is in neutral or i pull the clutch in and roll under 20 mph. At speed its fine and doesn't make any noise.
Hopefully i can give you an answer on friday.

The dealer said its not my gearbox on my bike he said it would be making the noise all the time and theres no play on the front sprocket shaft. Its moving nice and smooth.

Its a shame I loved the bike till i started dealing with this getting close trading it in and getting somethings else. Need something reliable to get to my work :(

Good luck, I think it's the chain that stretched on mine