I just did a valve clearance check and found one intake valve on the front cylinder a little tight. I replaced the shim and when I spun the engine (with the rear wheel) to confirm the clearance I heard a series of clicks. They appear to be coming from the timing chain area of the front cylinder and it seems to be when either the intake or exhaust valves are closing. It happens on every rotation at exactly the same points. The engine was locked when I removed the cams and everything times up properly. I took great care to ensure nothing fell into the engine and due to the precision timing of the sounds, am convinced that nothing has fallen in. The rear cylinder is quiet.

I've removed and re-installed the bridge, cams, bucket, and shim in that was replaced with no change.

I don't REMEMBER hearing this before but...

The rad and oil tank are off and after spinning the rear wheel a bit during the valve checks and now with this noise, I've probably pumped out most of the oil from the engine.

Here's a vid;

Have you oiled the shim before you put it back in?
It's a long shot, but my dad (mechanic with over 30 years experience) suggested this.