I'm not very familiar with landy Diesel engines, is the oil pump in the sump? Apart from the knocking does the engine start, tickover and rev nicely? Have you looked carefully all around the engine to make sure something isn't banging against it? I had a funny knocking noise and it turned out to be a mud shield knocking against the wing, didn't do it at certain revs.

Col
Starts, runs and revs really well
 
When you say vacuum pump I assume you mean for the brakes? This is a single line system, no servo, so the vacuum pump has had the vanes removed and is pretty silent.
Yes. Driven off the camshaft, and mounted where the distributor or fuel pump would be on a two and a quarter engine.
 

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