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Okay, got this one to work.
The Joint location is given by the child link origin which is specified as part of the "link " element at the root level. This joint origin needs to be specified in terms of the model origin (my model origin was at 0 0 0 0 0 0) so it could also be the global origin. Therefore you need to work out the positions of the joints initially in this coordinate frame. And it seems to work.
On a side note, this specifying joint locations in this manner is unconventional. The original urdf method of locating the joint in terms of the parent link in the parent links frame is far more conventional and widely used. It requires a lot less initial calculation to boot.
Peter
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