Every part of the drive line has a little slop. Add them all together and you get knocks and bangs, particularly in a manual. You have movement in the input shaft to the gearbox and the clutch plate, then you have movement within the gears within the transmission, then between the output shaft of the gearbox and the transfer case, slop within the gears within the transfer case, then slop in the centre diff, the drive shaft splines to the front and rear diff, then between the crown wheel and pinion, then in the spider gears, the the splines on the axles, the CVs and the then the splines to the axle to the wheels. But as they just had the transfer case out, I would suggest that it is in the output shaft from the transmission and the transfer case.
But as others have suggested, it could also be in the A frame ball joint, The upper A frame bushes. You said that you had replaced the trailing arm bushes, but did to replace the bolts as well. The bolts wear and allow the bush to move backward and forwards.
So in regard to clunks in a Landrover, you can pick any of the above. Good Luck.
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