Hi Joe,
I would use a G92 Home command. In the first setup, with the tool axis at home over the corner of the part, the corner of your part would be G92 X0 Y0 Zz
After repositioning, with the tool at home, the corner now becomes G92 X40. Y0 Zz
However, you will most certainly have to find a way to break all the toolpaths at the 40" mark in your CAD, and only create the paths on one side of the line for your first program, and paths on the second side for your second program. But that is not the end of it. You will have to allow a bit of overlap between the toolpaths at the 40" mark, so that the flats are properly cleaned up.
Take this advice cautiously, because I don't know how any of your setup works.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)