It is poor form to reply to your own post but...
According to the LinuxCNC docs at http://linuxcnc.org/docs/html/gcode/...sec:tool-table the tool table is a text file, They also say:
"Earlier versions of LinuxCNC had two different tool table formats for mills and lathes, but since the 2.4.x release, one tool table format is used for all machines. Just ignore the parts of the tool table that don’t pertain to your machine, or which you don’t need to use."
The normal LinuxCNC tool table has offsets for X, Y, Z, A, B, C, U, V, W-axis. If Tormach hasn't changed things then you could use G10 to setup the required offsets.
Could someone with a Duality verify that this works?