maybe for applying the stops on your jig using some kind of silicone would be a better option. this would allow for minor adjustments to get the stops right on the line before the glue sets up.
as far as the general method, the printer will always set the target. using cnc/laser is way more complex. print on the loading board the exact positions of the phone cases. possibly scan them with a ruler so that you can scale them exact for printing, moving the outlines around in photoshop to your liking. then lay in gator board or if you really want to do it slick possibly use some kind of translucent silicone mold compound. or lay down a thick layer of clear silicone, wipe vaseline on the back of a phone case. let it set up then pull the phone case up. that should leave a cradle that is a copy of the phone case's shape.