I think I missed something, why are you rezeroing X/Y/Z after you place your stock? You should only rezero Z and drill the exact same 2 holes, flip the piece over and align with pins and drill the exact same two holes(don’t go so deep that you hit the pins). Do the rest of your side 1 machining, flip and do side 2. If you do that you should be spot on every time. I’ve done a few of these this way using ground steel pins and tight fitting holes and it doesn’t shift unless I do something wrong.
i want to reuse those holes for future projects and i may have recentered for other projects.
maybe i should just use the rapid position in the center of board for so i can get back or save my coordinates.
do you always drill new holes if your zero has been reset?