Thanks guys for your help,
I understood everything but "Set the port and pin of the C axis for the spindle output" I'm not sure how this works with the G100 which only uses the step and dir ports rather than pins.
So i did everything else you suggested which has made a lot of progress. I have set X,Y,Z,A,B,S axes and now the spindle responds to M03 commands and stops when the onscreen controls are used. However one problem still remains which is i cannot tune the spindle as any changes made on the motor tuning screen for the spindle are not saved or flashed successfully. (this is kind of important as the accel is set too high at the moment). All the other axes (X and Z) can be tuned fine.
Also the onscreen display can't see the encoder (which i really couldn't care less about) but the spindle autocal can't see the encoder either which i can probably live without as well if i can tune the motor)
Any ideas on this?
Lost Tourist