Has anyone had problems with input shaft failure or other gearbox problems on late ('53 reg) defenders? I had one go and can't get it accepted under warranty as it had no oil in it by the time it was recovered to the main dealer . If it is a common problem I can fuel my arguement, can anyone help? I know it had oil in it at the time of failure and can only guess it dumped it after it failed.

It shouldn't be too hard to prove that the oil leaked out after/at the point of failure...but even if there was no oil in and that's why it failed, it shouldn't have dumped its oil anyway. You should be able to claim from that approach.
(unless the casing was damaged,for instance by off-road use)