If you’re looking to automate then replacing your manual zero with a good automatic will be an effort saver once you’re confident it works.
To maintain relative position of the four jig locations I’d suggest making up a single full jig which has all four workstations on a single spoilboard so that you don’t have to probe for zero four times, if you machine the jig on the Shapeoko then you know where the four jig locations are relative to each other and you just need to make sure the jig is on the machine square.
As for a single file, you could go about it the ‘easy’ way and set up four instances of your workpiece in your CAM spaced out as they are on the machine and then just set up tool paths to cut all of them. Or you could venture into multiple work coordinate systems in your CAM (assuming you have Fusion or similar) and then tell the Shapeoko where your four jigs are, see this thread for some info
I have not done multiple WCS so I’ll leave it to others to say whether it’s worth the effort through Carbide Motion or not.