My 110 defender as a bit of a clonk when changing up it only seems to do it between 2nd and 3rd and coming down is ok i have tried slowly let out the clutch is helps a bit, it feels like it is coming from behind me when driving.
Well next moove i'll gues is to try the UJ's , and/or even take the PTO cover to look at the g box main shaft splines, ps while at the A frame did you check for any moovement on the bush end.
Granted, it might seem tight when your prodding it by hand but once you have a 1750kg Landy exerting force on the components it can soon start to clonk. Sometimes a pry-bar is a good idea to see what will move excessively under force.
Park it on the flat, lie under it and have a mate roll it back and forward a bit while you watch all the bushes and joints. I have the same problem, if I roll the Landy back and forward I can hear it clonking away. I will work out exactly what it is soon, I suspect the A-frame bushes or ball joint.