VisMach CAD vs. Joint Origin

I have a 5-DOF robot Cad model.  I exported each link with the same world origin.

In the VisMach script Is there a way to translate the link origin and part independently.  For example move the link origin to line up with the joint axis then reposition the cad back to the correct physical position?

 

You can certainly translate/rotate the stl to the desired position in vismach before attaching it to your model.
However it is much easier if each stl has it's origin in a suitable position when it is imported into vismach.
You'll need to take care of that before you export the stl from the cad. In solidworks for example you can create alternative origins on your part and then choose the appropriate one in the export dialog.

That is what I'll do.

Another question, what is the difference or use of Rotate vs. Hal-rotate? setting up the Cad.

rotate/translate is for use with static values to setup the model.
hal-rotate/-translate is to move the model using hal-pin values.