Phew that sounds nasty! I'd have gone with the sidestand too Martyn - just checking it's not April 1st!
I suggest putting the bike on a box/stand so the back wheel is off the ground and put a lever under the rear wheel to lift and lower it. Get someone to hang onto the bike though - it's hard to keep it steady and lever the wheel and look/listen for movement in the linkages.
Does the clunk happen at full drop of the wheel, or as you push down? It's hard to tell from your vid.
Check the spring seats too. Have you got all the preload wound off? (adjuster nut screwed all the way to the top) Could even be the damper shaft broken or loose inside the shock body (had this on an xtz660 once) Sorry to be the merchant of doom
I removed the side stand completely.
It took me an hour or two to remove the rear suspension relay arm. One bolt was stuck. You probably know which one :). There is a small free play in the bearing. So far I changed one bearing the lower one (all balls 29-5013). It did not make any difference. The problem still persists.
Yes, I tried adjusting the preloading turning it completely clockwise and anticlockwise. It looked to me it does not make any difference, i.e. I did not notice if shock decompression changes from slow to fast of vice verse.
I'm thinking the problem can be with rear suspension itself. Looks like the sound comes when releasing suspension i.e. spring starts return to its position. I'm gonna change the rest of two bearings of relay arm.
It is good that I have two more TTRs. So, I could move parts from one to another and identify the problem.
I'm not sure what you mean "spring being wound off". It does not make sense how google translator translate it in my local language :)
Spring appears having purple color instead of yellow. Not sure if this purple is result of painting stock spring or some kind of aftermarket:
Spring preload is adjusted by the thread that runs up the shock absorber body (at the top). "Spring wound off" means the rings that run on this thread are unscrewed to the top of the shock (There are 2 - one that touches the top of the spring, and a slightly smaller one that tightens against it to lock it in position.) This would mean the spring is at it's softest and is maybe allowing the spring seat to move.
The part you turned clockwise and anticlockwise sounds to me like the compression damping adjustment on the cannister next to the solenoid (right hand side, bottom rear corner of the tank), or perhaps the rebound damping adjustment screw to be found at the bottom of the shock below the spring? (Someone who can do pictures and arrows please feel free to add some) These adjust the valves inside to change the speed the shock absorber reacts at and are nothing to do with preload.
I think you would be able to see massive movement in the linkages if they were the cause of this noise, so I still suspect either the spring seats moving, or the centre shaft of the shock absorber either broken or coming apart inside.