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It doesn't sound like a fuel system at all, I'd remove glow plugs to see if they're complete, and if you can do the compression test.
The knocking sound indicates something mechanical, has the timing belt jumped a tooth out so if piston is hitting a valve...? I'd make sure valve clearance is correct as well.
Does the engine smoke? blueish or greyish?
The noise sound very much like either big end or piston knocking but from the video the engine seems to run smoothly so isn't something like rotating outside being hit e.g flywheel bolt/clutch etc.
What happens when you de clutch?
Also can you narrow down where is the knock coming from, is it from the top, bottom etc. You can fashion up temporary stethoscope from long screwdriver which you can point against the engine section and by holding it where part of you hand/palm protrudes over the handle and act like cup you can put your ear against. You should be able to hear clearer where is that knocking sound coming louder from.
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