At a guess I'd say that the knock is caused by wear in one of the Universal Joints in the rear propshaft. The noise is the slack being taken up in the system as the transmission comes under load. It went away when you removed the rear propshaft because (obviously) you had no UJs on at the time.
Replacment UJs are quite cheap (£15-25), easy to replace and the best pattern-part ones to use are Hardy Spicer ones- I now have them all-round and quality is good.
Jack
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