Erratic knock from cylinder head
 

I've finally got my '97 XT600 running after rebuilding the bottom end. Sadly the knock that was one of the reasons I did the work in the first place is still there.
If anyone has a minute to listen to the video and identify what the noise might be, and whether it is serious, I would be very grateful. https://youtu.be/WV7aPlAHZh4
It is an erratic sound that happens at low revs, just above idle, is distinct enough to feel through the handlebars and seems to be coming from the top end.
The spinning bit you can see on the left of the screen is the remains of the rev counter cable which I have removed. The noise is definitely not coming from there or from the bearings, woodruff keys etc in the crankcase which are brand new. As I said above this noise was occurring before I did the work.
Thanks in advance for any help.

Take a wooden stick, and place one end to different parts of rhe engine case and the other to your ear, you should hear the difference, the closer to the knocking sound the louder will be. This is no joke ;) Try it!

Good idea. I will try the wooden stick trick today. I put a homemade stethoscope on it and couldn't identify any specific part of the engine it was coming from. If anything it seemed more noticeable when I held the steth wand against the frame just behind the oil tank. I made a slightly longer video that gives more of a listen to the tapping. https://youtu.be/Tr-CHN-KuWA

Large screwdriver works too, doesnt sound good at all. Are the valve clearence ok?

I've checked the clearances again and they're ok. I've been working through the other possibilities and it occurred to me that maybe the sound is coming from the little end - maybe not enough lubrication getting through to the piston pin. Does that sound likely to anyone?

The pin looked ok when I had it apart so that was one thing I did not change - which was possible a bad decision. It seems strange that there is no bearing on the little end. I can't thing of what else it might be - the crankcase bearings are all new, cam chain is new, tensioner is working and I have replaced all the crankcase bearings and redone the big end with new bearing, conrod and crank pin.